From 6bf00c0c3ad93859725101268d9eb57ab3aeb8a9 Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 16:57:03 +0200 Subject: [PATCH 1/6] update linting --- .flake8 | 3 +++ .github/workflows/lint.yml | 30 +++++++++--------------------- .isort.cfg | 2 ++ .markdownlint.yaml | 10 ++++++++++ .trunk/.gitignore | 3 +++ .trunk/trunk.yaml | 14 ++++++++++++++ 6 files changed, 41 insertions(+), 21 deletions(-) create mode 100644 .flake8 create mode 100644 .isort.cfg create mode 100644 .markdownlint.yaml create mode 100644 .trunk/.gitignore create mode 100644 .trunk/trunk.yaml diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..5ba6e2f --- /dev/null +++ b/.flake8 @@ -0,0 +1,3 @@ +# Autoformatter friendly flake8 config (all formatting rules disabled) +[flake8] +extend-ignore = D1, D2, E1, E2, E3, E501, W1, W2, W3, W5 diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 10b971f..dc5ac56 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -1,25 +1,13 @@ -name: python lint -on: - ['push', 'pull_request'] +name: lint + +on: pull_request + jobs: build: - runs-on: ${{ matrix.platform }} - strategy: - matrix: - platform: [ubuntu-latest] - python-version: [3.7] - steps: - - uses: actions/checkout@v2 + runs-on: ubuntu-latest - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2.2.2 - with: - python-version: ${{ matrix.python-version }} - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install black + steps: + - uses: actions/checkout@v3 - - name: black - run: black --check --diff . + - name: Trunk Check + uses: trunk-io/trunk-action@v1 diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 0000000..b9fb3f3 --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,2 @@ +[settings] +profile=black diff --git a/.markdownlint.yaml b/.markdownlint.yaml new file mode 100644 index 0000000..fb94039 --- /dev/null +++ b/.markdownlint.yaml @@ -0,0 +1,10 @@ +# Autoformatter friendly markdownlint config (all formatting rules disabled) +default: true +blank_lines: false +bullet: false +html: false +indentation: false +line_length: false +spaces: false +url: false +whitespace: false diff --git a/.trunk/.gitignore b/.trunk/.gitignore new file mode 100644 index 0000000..507283d --- /dev/null +++ b/.trunk/.gitignore @@ -0,0 +1,3 @@ +*out +*logs +external diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml new file mode 100644 index 0000000..17ec10a --- /dev/null +++ b/.trunk/trunk.yaml @@ -0,0 +1,14 @@ +version: 0.1 +cli: + version: 0.15.1-beta +lint: + enabled: + - actionlint@1.6.15 + - black@22.6.0 + - flake8@5.0.2 + - git-diff-check@SYSTEM + - gitleaks@8.9.0 + - isort@5.10.1 + - markdownlint@0.32.1 + - prettier@2.7.1 + - taplo@release-taplo-cli-0.6.8 From 0cfc1e1044b0abf990b251c85ffa21afca1b8b0a Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 17:29:33 +0200 Subject: [PATCH 2/6] change bmrb table to NMR-START v3.1 also add a feature to align the input sequence with the sequence present in the BMRB file --- .gitignore | 2 +- example/1ubq-bmrb-tables.txt | 946 ------------- example/1ubq-seq.txt | 1 - example/1ubq.pdb | 983 ------------- example/1ubq.ss | 1 - example/bmr18583_3.str | 1945 ++++++++++++++++++++++++++ example/input.toml | 23 +- requirements.txt | 1 + src/fandas/cli.py | 36 +- src/fandas/modules/bmrb.py | 102 ++ src/fandas/modules/chemical.py | 47 +- src/fandas/modules/chemical_shift.py | 69 +- src/fandas/modules/input.py | 18 +- src/fandas/modules/utils.py | 30 +- tests/__init__.py | 2 +- tests/data/test_bmrm.str | 1945 ++++++++++++++++++++++++++ tests/data/test_input.toml | 18 +- tests/modules/test_bmrb.py | 50 + tests/modules/test_chemical_shift.py | 18 +- tests/modules/test_experiment.py | 14 +- tests/modules/test_input.py | 6 +- tests/modules/test_utils.py | 55 +- 22 files changed, 4187 insertions(+), 2125 deletions(-) delete mode 100644 example/1ubq-bmrb-tables.txt delete mode 100644 example/1ubq-seq.txt delete mode 100644 example/1ubq.pdb delete mode 100644 example/1ubq.ss create mode 100644 example/bmr18583_3.str create mode 100644 src/fandas/modules/bmrb.py create mode 100644 tests/data/test_bmrm.str create mode 100644 tests/modules/test_bmrb.py diff --git a/.gitignore b/.gitignore index c31c3f7..7cc0ee0 100644 --- a/.gitignore +++ b/.gitignore @@ -155,5 +155,5 @@ cython_debug/ .vscode/ # Project-specific -example/*_exp.txt +example/*_exp*.txt debug/* diff --git a/example/1ubq-bmrb-tables.txt b/example/1ubq-bmrb-tables.txt deleted file mode 100644 index 1b469e4..0000000 --- a/example/1ubq-bmrb-tables.txt +++ /dev/null @@ -1,946 +0,0 @@ -1 M C 170.5200 -1 M CA 54.4000 -1 M CB 33.4599 -1 M CE 17.6847 -1 M CG 31.8754 -1 M H 8.2666 -1 M HA 4.2200 -1 M HB2 2.0700 -1 M HB3 2.1390 -1 M HE 1.8684 -1 M HG2 2.4714 -1 M HG3 2.2222 -1 M N 120.7947 -2 Q C 175.8389 -2 Q CA 54.9000 -2 Q CB 30.8000 -2 Q CD 180.0738 -2 Q CG 34.2460 -2 Q H 8.8200 -2 Q HA 5.2700 -2 Q HB2 1.6912 -2 Q HB3 1.8633 -2 Q HE21 6.8242 -2 Q HE22 7.4657 -2 Q HG2 2.1938 -2 Q HG3 2.0026 -2 Q N 125.0800 -3 I C 171.6200 -3 I CA 59.5000 -3 I CB 42.4000 -3 I CD1 14.3000 -3 I CG1 25.4000 -3 I CG2 18.1000 -3 I H 8.3300 -3 I HA 4.2100 -3 I HB 1.7662 -3 I HD1 0.6100 -3 I HG2 0.6600 -3 I HG12 0.9428 -3 I HG13 1.1000 -3 I N 116.0800 -4 F C 175.2200 -4 F CA 54.6000 -4 F CB 41.2000 -4 F CD1 132.3000 -4 F CD2 131.9850 -4 F CE1 131.2000 -4 F CE2 131.0049 -4 F CG 139.9524 -4 F CZ 129.4000 -4 F H 8.5700 -4 F HA 5.6100 -4 F HB2 2.8800 -4 F HB3 3.0422 -4 F HD1 7.1100 -4 F HD2 7.1100 -4 F HE1 7.2800 -4 F HE2 7.2701 -4 F HZ 7.2800 -4 F N 118.5800 -5 V C 174.3200 -5 V CA 60.7000 -5 V CB 34.7579 -5 V CG1 21.3485 -5 V CG2 21.7287 -5 V H 9.2600 -5 V HA 4.7900 -5 V HB 1.9300 -5 V HG1 0.7100 -5 V HG2 0.7600 -5 V N 120.7885 -6 K C 177.3016 -6 K CA 54.3000 -6 K CB 35.5000 -6 K CD 29.4536 -6 K CE 42.0471 -6 K CG 24.9080 -6 K H 8.8700 -6 K HA 5.3400 -6 K HB2 1.6306 -6 K HB3 1.6890 -6 K HD2 1.6000 -6 K HD3 1.6113 -6 K HE2 2.9200 -6 K HE3 2.9200 -6 K HG2 1.3365 -6 K HG3 1.4319 -6 K HZ 7.5356 -6 K N 128.3800 -7 T C 175.9775 -7 T CA 60.5000 -7 T CB 70.4000 -7 T CG2 21.7000 -7 T H 8.6900 -7 T HA 5.0000 -7 T HB 4.8000 -7 T HG2 1.2001 -7 T N 118.1800 -8 L C 177.5919 -8 L CA 57.0878 -8 L CB 41.5675 -8 L CD1 25.1652 -8 L CD2 23.9923 -8 L CG 27.0114 -8 L H 8.9100 -8 L HA 4.3300 -8 L HB2 1.9314 -8 L HB3 1.7641 -8 L HD1 1.0000 -8 L HD2 0.9836 -8 L HG 1.9000 -8 L N 121.7076 -9 T C 175.1165 -9 T CA 61.1382 -9 T CB 68.8508 -9 T CG2 21.6695 -9 T H 7.5900 -9 T HA 4.4100 -9 T HB 4.5835 -9 T HG2 1.2125 -9 T N 106.0812 -10 G C 173.8614 -10 G CA 45.7890 -10 G H 7.7800 -10 G HA 3.9393 -10 G HA2 3.8828 -10 G HA3 3.8846 -10 G N 109.5726 -11 K C 175.5440 -11 K CA 56.0078 -11 K CB 33.5134 -11 K CD 29.1482 -11 K CE 41.9656 -11 K CG 25.0257 -11 K H 7.2500 -11 K HA 4.3700 -11 K HB2 1.7300 -11 K HB3 1.8100 -11 K HD2 1.6600 -11 K HD3 1.6600 -11 K HE2 2.9500 -11 K HE3 2.9500 -11 K HG2 1.2935 -11 K HG3 1.4061 -11 K HZ 7.5757 -11 K N 121.8156 -12 T C 174.0200 -12 T CA 62.2000 -12 T CB 69.5068 -12 T CG2 22.0705 -12 T H 8.5000 -12 T HA 5.0800 -12 T HB 3.9800 -12 T HG2 1.1895 -12 T N 121.5282 -13 I C 175.4200 -13 I CA 60.2000 -13 I CB 41.2000 -13 I CD1 14.8000 -13 I CG1 27.3000 -13 I CG2 17.6000 -13 I H 9.4400 -13 I HA 4.5300 -13 I HB 1.8900 -13 I HD1 0.7500 -13 I HG2 0.9000 -13 I HG12 1.1200 -13 I HG13 1.4016 -13 I N 127.9800 -14 T C 173.5200 -14 T CA 62.2000 -14 T CB 69.6000 -14 T CG2 22.4194 -14 T H 8.5700 -14 T HA 4.9700 -14 T HB 4.0500 -14 T HG2 1.2276 -14 T N 121.8800 -15 L C 174.7200 -15 L CA 52.8000 -15 L CB 47.3000 -15 L CD1 26.7455 -15 L CD2 24.1000 -15 L CG 27.3000 -15 L H 8.6700 -15 L HA 4.7500 -15 L HB2 1.3800 -15 L HB3 1.2600 -15 L HD1 0.7400 -15 L HD2 0.7900 -15 L HG 1.4500 -15 L N 124.6800 -16 E C 175.8200 -16 E CA 54.8000 -16 E CB 29.9000 -16 E CD 182.5095 -16 E CG 35.8255 -16 E H 8.0828 -16 E HA 4.9200 -16 E HB2 1.8700 -16 E HB3 1.9400 -16 E HG2 2.2500 -16 E HG3 2.1100 -16 E N 122.6800 -17 V C 174.3200 -17 V CA 58.5000 -17 V CB 35.8000 -17 V CG1 22.2000 -17 V CG2 19.8000 -17 V H 8.8500 -17 V HA 4.7100 -17 V HB 2.3165 -17 V HG1 0.6379 -17 V HG2 0.6717 -17 V N 119.0800 -18 E C 176.4200 -18 E CA 52.6000 -18 E CB 30.8000 -18 E CD 183.0147 -18 E CG 36.1000 -18 E H 8.6800 -18 E HA 5.0800 -18 E HB2 1.9197 -18 E HB3 1.6700 -18 E HG2 2.3800 -18 E HG3 2.2700 -18 E N 119.4800 -19 P C 175.2200 -19 P CA 65.1000 -19 P CB 32.2000 -19 P CD 50.4000 -19 P CG 28.0000 -19 P HA 4.1600 -19 P HB2 2.0604 -19 P HB3 2.1076 -19 P HD2 3.8200 -19 P HD3 3.8865 -19 P HG2 2.0900 -19 P HG3 2.0818 -20 S C 173.7086 -20 S CA 57.0000 -20 S CB 63.6000 -20 S H 7.5269 -20 S HA 4.3800 -20 S HB2 4.1509 -20 S HB3 3.8100 -20 S N 104.2215 -21 D C 176.2200 -21 D CA 55.2000 -21 D CB 40.5903 -21 D CG 179.4221 -21 D H 7.9800 -21 D HA 4.7000 -21 D HB2 2.6147 -21 D HB3 2.7804 -21 D N 125.2800 -22 T C 176.8200 -22 T CA 60.4000 -22 T CB 71.8353 -22 T CG2 22.1000 -22 T H 7.8699 -22 T HA 4.9500 -22 T HB 4.8000 -22 T HG2 1.2956 -22 T N 110.5800 -23 I C 178.4200 -23 I CA 62.0000 -23 I CB 35.0000 -23 I CD1 9.2501 -23 I CG1 27.2000 -23 I CG2 18.0000 -23 I H 8.5100 -23 I HA 3.6600 -23 I HB 2.2375 -23 I HD1 0.6100 -23 I HG2 0.8100 -23 I HG12 1.3200 -23 I HG13 1.4671 -23 I N 119.7040 -24 E C 178.7200 -24 E CA 59.9000 -24 E CB 28.0738 -24 E CD 182.5863 -24 E CG 36.0767 -24 E H 9.5834 -24 E HA 3.9200 -24 E HB2 2.0700 -24 E HB3 2.0700 -24 E HG2 2.3700 -24 E HG3 2.4048 -24 E N 119.3800 -25 N C 176.9341 -25 N CA 55.9000 -25 N CB 38.2000 -25 N CG 176.5498 -25 N H 7.8700 -25 N HA 4.5600 -25 N HB2 2.8800 -25 N HB3 2.9983 -25 N HD21 7.5438 -25 N HD22 7.0242 -25 N N 118.5800 -26 V C 178.2200 -26 V CA 67.9000 -26 V CB 31.0000 -26 V CG1 22.4727 -26 V CG2 22.4823 -26 V H 8.0400 -26 V HA 3.4100 -26 V HB 2.3564 -26 V HG1 0.7696 -26 V HG2 0.8542 -26 V N 119.1092 -27 K C 180.3200 -27 K CA 59.3000 -27 K CB 33.4548 -27 K CD 29.4833 -27 K CE 42.3500 -27 K CG 26.0347 -27 K H 8.5200 -27 K HA 4.5700 -27 K HB2 2.0100 -27 K HB3 1.8767 -27 K HD2 1.6348 -27 K HD3 1.7051 -27 K HE2 2.8921 -27 K HE3 2.8321 -27 K HG2 1.4669 -27 K HG3 1.4133 -27 K HZ 6.9991 -27 K N 117.0800 -28 A C 180.6200 -28 A CA 55.7000 -28 A CB 18.7000 -28 A H 8.0200 -28 A HA 4.1700 -28 A HB 1.6337 -28 A HB2 1.8587 -28 A HB3 1.4502 -28 A N 125.1605 -29 K C 180.5200 -29 K CA 60.5000 -29 K CB 33.3000 -29 K CD 29.8039 -29 K CE 42.3609 -29 K CG 25.6612 -29 K H 7.8400 -29 K HA 4.2200 -29 K HB2 2.1600 -29 K HB3 2.0391 -29 K HD2 1.5310 -29 K HD3 1.7783 -29 K HE2 3.0300 -29 K HE3 3.0005 -29 K HG2 1.6100 -29 K HG3 1.5679 -29 K HZ 7.4248 -29 K N 121.7800 -30 I C 178.3200 -30 I CA 66.1000 -30 I CB 36.8917 -30 I CD1 15.4469 -30 I CG1 30.9214 -30 I CG2 16.7044 -30 I H 8.2400 -30 I HA 3.5200 -30 I HB 2.2405 -30 I HD1 0.8893 -30 I HG2 0.7000 -30 I HG12 1.5981 -30 I HG13 1.0803 -30 I N 121.7800 -31 Q C 178.9200 -31 Q CA 59.6000 -31 Q CB 27.9000 -31 Q CD 179.6799 -31 Q CG 33.9794 -31 Q H 8.5400 -31 Q HA 3.8400 -31 Q HB2 2.0693 -31 Q HB3 2.2822 -31 Q HE21 7.0298 -31 Q HE22 7.2940 -31 Q HG2 2.3500 -31 Q HG3 2.3500 -31 Q N 125.0008 -32 D C 176.7150 -32 D CA 56.2000 -32 D CB 41.7000 -32 D CG 179.3687 -32 D H 7.9400 -32 D HA 4.3600 -32 D HB2 2.7800 -32 D HB3 2.8315 -32 D N 118.4800 -33 K C 177.9200 -33 K CA 58.7000 -33 K CB 34.3000 -33 K CD 29.7000 -33 K CE 41.6000 -33 K CG 24.8856 -33 K H 7.4870 -33 K HA 4.3400 -33 K HB2 2.0200 -33 K HB3 1.8800 -33 K HD2 1.7400 -33 K HD3 1.6400 -33 K HE2 3.1160 -33 K HE3 3.0703 -33 K HG2 1.5749 -33 K HG3 1.5066 -33 K HZ 7.4053 -33 K N 113.9626 -34 E C 178.1375 -34 E CA 55.6000 -34 E CB 32.8000 -34 E CD 182.5386 -34 E CG 35.9054 -34 E H 8.6900 -34 E HA 4.6100 -34 E HB2 2.0104 -34 E HB3 1.9865 -34 E HG2 2.1384 -34 E HG3 2.1800 -34 E N 113.8348 -35 G C 173.2200 -35 G CA 45.6000 -35 G H 8.4500 -35 G HA 3.9723 -35 G HA2 3.9500 -35 G HA3 4.0326 -35 G N 110.4800 -36 I C 173.0639 -36 I CA 57.8000 -36 I CB 39.9551 -36 I CD1 14.1000 -36 I CG1 27.7000 -36 I CG2 17.7000 -36 I H 6.2828 -36 I HA 4.4500 -36 I HB 1.4600 -36 I HD1 0.8000 -36 I HG2 0.9600 -36 I HG12 1.1837 -36 I HG13 1.3657 -36 I N 120.3800 -37 P C 176.5200 -37 P CA 61.7000 -37 P CB 32.1000 -37 P CD 50.9000 -37 P CG 28.0671 -37 P HA 4.6600 -37 P HB2 2.1515 -37 P HB3 2.1251 -37 P HD2 3.7198 -37 P HD3 3.8110 -37 P HG2 2.0500 -37 P HG3 2.1000 -38 P C 178.2200 -38 P CA 66.4000 -38 P CB 33.2057 -38 P CD 51.0784 -38 P CG 27.9000 -38 P HA 4.1400 -38 P HB2 2.1033 -38 P HB3 2.2040 -38 P HD2 3.7800 -38 P HD3 3.8589 -38 P HG2 2.0633 -38 P HG3 1.9775 -39 D C 176.5200 -39 D CA 55.5000 -39 D CB 40.6000 -39 D CG 179.5171 -39 D H 8.4900 -39 D HA 4.4400 -39 D HB2 2.7000 -39 D HB3 2.7900 -39 D N 112.9800 -40 Q C 175.1200 -40 Q CA 55.5000 -40 Q CB 29.7000 -40 Q CD 179.8240 -40 Q CG 34.3473 -40 Q H 7.7800 -40 Q HA 4.4600 -40 Q HB2 2.0363 -40 Q HB3 1.8500 -40 Q HE21 7.1907 -40 Q HE22 7.1697 -40 Q HG2 2.4000 -40 Q HG3 2.4000 -40 Q N 116.8800 -41 Q C 176.4811 -41 Q CA 55.9000 -41 Q CB 31.2316 -41 Q CD 178.5747 -41 Q CG 33.7723 -41 Q H 7.4100 -41 Q HA 4.3200 -41 Q HB2 1.9000 -41 Q HB3 1.9700 -41 Q HE21 6.8308 -41 Q HE22 6.8157 -41 Q HG2 2.5080 -41 Q HG3 2.1912 -41 Q N 118.4800 -42 R C 174.2200 -42 R CA 54.6000 -42 R CB 32.8923 -42 R CD 43.3105 -42 R CG 26.6477 -42 R CZ 159.5196 -42 R H 8.4900 -42 R HA 4.5000 -42 R HB2 1.6748 -42 R HB3 1.7300 -42 R HD2 3.1600 -42 R HD3 3.1123 -42 R HE 7.1228 -42 R HG2 1.4623 -42 R HG3 1.5594 -42 R N 122.0818 -43 L C 175.4200 -43 L CA 52.7000 -43 L CB 45.6358 -43 L CD1 26.5726 -43 L CD2 24.1000 -43 L CG 27.1000 -43 L H 8.7400 -43 L HA 5.3500 -43 L HB2 1.5900 -43 L HB3 1.1900 -43 L HD1 0.7900 -43 L HD2 0.8200 -43 L HG 1.5000 -43 L N 123.7123 -44 I C 176.0200 -44 I CA 59.0000 -44 I CB 41.9780 -44 I CD1 13.9410 -44 I CG1 28.4621 -44 I CG2 17.7000 -44 I H 9.0500 -44 I HA 4.9600 -44 I HB 1.7400 -44 I HD1 0.7000 -44 I HG2 0.7100 -44 I HG12 1.1131 -44 I HG13 1.3389 -44 I N 122.6800 -45 F C 174.2200 -45 F CA 58.4706 -45 F CB 43.9000 -45 F CD1 132.5000 -45 F CD2 131.2184 -45 F CE1 131.0000 -45 F CE2 130.7590 -45 F CG 138.9752 -45 F CZ 129.9894 -45 F H 8.8200 -45 F HA 5.1100 -45 F HB2 2.8573 -45 F HB3 2.6411 -45 F HD1 7.2348 -45 F HD2 7.3357 -45 F HE1 7.5268 -45 F HE2 7.5297 -45 F HZ 7.4815 -45 F N 125.1800 -46 A C 177.9200 -46 A CA 51.9000 -46 A CB 17.1000 -46 A H 8.7700 -46 A HA 3.7000 -46 A HB 0.9121 -46 A HB2 1.8951 -46 A HB3 1.6562 -46 A N 132.4800 -47 G C 173.5200 -47 G CA 45.6000 -47 G H 8.0336 -47 G HA 3.7671 -47 G HA2 4.1000 -47 G HA3 3.4714 -47 G N 102.8800 -48 K C 174.7200 -48 K CA 54.2000 -48 K CB 34.9000 -48 K CD 29.1000 -48 K CE 42.1935 -48 K CG 24.7044 -48 K H 7.9900 -48 K HA 4.6100 -48 K HB2 1.9807 -48 K HB3 1.9123 -48 K HD2 1.7400 -48 K HD3 1.6065 -48 K HE2 3.1737 -48 K HE3 3.1406 -48 K HG2 1.5121 -48 K HG3 1.4244 -48 K HZ 7.5231 -48 K N 120.6800 -49 Q C 176.0200 -49 Q CA 56.1000 -49 Q CB 28.5287 -49 Q CD 179.7280 -49 Q CG 34.4421 -49 Q H 8.5400 -49 Q HA 4.5800 -49 Q HB2 2.0123 -49 Q HB3 2.0400 -49 Q HE21 7.1436 -49 Q HE22 7.2506 -49 Q HG2 2.2760 -49 Q HG3 2.2455 -49 Q N 122.4800 -50 L C 176.8200 -50 L CA 54.5000 -50 L CB 40.9219 -50 L CD1 26.1000 -50 L CD2 22.6343 -50 L CG 26.5549 -50 L H 8.4800 -50 L HA 4.0800 -50 L HB2 1.5200 -50 L HB3 1.0500 -50 L HD1 0.4869 -50 L HD2 0.0630 -50 L HG 1.4800 -50 L N 128.2800 -51 E C 175.3082 -51 E CA 56.2000 -51 E CB 32.4979 -51 E CD 182.5850 -51 E CG 35.8989 -51 E H 8.3107 -51 E HA 4.4900 -51 E HB2 2.0171 -51 E HB3 2.2428 -51 E HG2 2.3700 -51 E HG3 2.4346 -51 E N 124.3800 -52 D C 176.7200 -52 D CA 56.2206 -52 D CB 40.6103 -52 D CG 179.4440 -52 D H 8.0969 -52 D HA 4.3600 -52 D HB2 2.7900 -52 D HB3 2.7238 -52 D N 122.0800 -53 G C 174.3200 -53 G CA 44.9000 -53 G H 9.3811 -53 G HA 3.9847 -53 G HA2 4.0300 -53 G HA3 4.0663 -53 G N 105.8796 -54 R C 175.4200 -54 R CA 53.8000 -54 R CB 32.8000 -54 R CD 43.2233 -54 R CG 27.3000 -54 R CZ 159.6592 -54 R H 7.4300 -54 R HA 4.7300 -54 R HB2 2.1300 -54 R HB3 1.8327 -54 R HD2 3.0930 -54 R HD3 3.1133 -54 R HE 7.0800 -54 R HG2 1.6500 -54 R HG3 1.7339 -54 R N 119.1800 -55 T C 176.5200 -55 T CA 59.5000 -55 T CB 72.4444 -55 T CG2 22.6544 -55 T H 8.7500 -55 T HA 5.2200 -55 T HB 4.5400 -55 T HG2 1.1715 -55 T N 109.3800 -56 L C 180.3200 -56 L CA 58.7000 -56 L CB 40.5000 -56 L CD1 26.6285 -56 L CD2 22.6486 -56 L CG 26.9266 -56 L H 8.1300 -56 L HA 4.0600 -56 L HB2 2.0688 -56 L HB3 1.2842 -56 L HD1 0.6500 -56 L HD2 0.7800 -56 L HG 1.7400 -56 L N 118.1908 -57 S C 178.3200 -57 S CA 61.6000 -57 S CB 62.5000 -57 S H 8.3800 -57 S HA 4.2700 -57 S HB2 3.8029 -57 S HB3 3.8700 -57 S N 113.1800 -58 D C 177.7200 -58 D CA 57.7000 -58 D CB 40.4000 -58 D CG 179.4824 -58 D H 7.8800 -58 D HA 4.3100 -58 D HB2 2.5415 -58 D HB3 2.2442 -58 D N 125.2800 -59 Y C 174.2200 -59 Y CA 59.0000 -59 Y CB 40.1566 -59 Y CD1 133.0000 -59 Y CD2 133.1835 -59 Y CE1 118.3407 -59 Y CE2 118.0011 -59 Y CG 133.0000 -59 Y CZ 159.9445 -59 Y H 7.2400 -59 Y HA 4.6400 -59 Y HB2 3.1876 -59 Y HB3 2.8786 -59 Y HD1 7.2539 -59 Y HD2 7.0865 -59 Y HE1 6.9200 -59 Y HE2 6.8196 -59 Y N 115.4800 -60 N C 173.4559 -60 N CA 53.0962 -60 N CB 37.3000 -60 N CG 177.7825 -60 N H 8.1200 -60 N HA 4.3700 -60 N HB2 3.0876 -60 N HB3 2.7617 -60 N HD21 7.4548 -60 N HD22 6.8864 -60 N N 118.5800 -61 I C 175.0200 -61 I CA 61.9000 -61 I CB 37.1000 -61 I CD1 14.8146 -61 I CG1 28.4000 -61 I CG2 16.9256 -61 I H 7.1900 -61 I HA 3.4100 -61 I HB 1.4300 -61 I HD1 0.4100 -61 I HG2 0.5000 -61 I HG12 0.8552 -61 I HG13 1.1400 -61 I N 117.6800 -62 Q C 176.3844 -62 Q CA 53.8000 -62 Q CB 31.3564 -62 Q CD 179.9782 -62 Q CG 34.1875 -62 Q H 7.5567 -62 Q HA 4.5100 -62 Q HB2 1.9508 -62 Q HB3 2.0800 -62 Q HE21 7.1771 -62 Q HE22 7.1083 -62 Q HG2 2.3300 -62 Q HG3 2.4000 -62 Q N 127.5800 -63 K C 175.2381 -63 K CA 57.5000 -63 K CB 32.8000 -63 K CD 29.0124 -63 K CE 42.0000 -63 K CG 23.8862 -63 K H 8.3600 -63 K HA 4.0000 -63 K HB2 1.9200 -63 K HB3 1.9567 -63 K HD2 1.7600 -63 K HD3 1.7600 -63 K HE2 3.0600 -63 K HE3 3.0600 -63 K HG2 1.5200 -63 K HG3 1.5200 -63 K HZ 7.4425 -63 K N 119.9800 -64 E C 174.5518 -64 E CA 58.4000 -64 E CB 26.3000 -64 E CD 182.6579 -64 E CG 36.5867 -64 E H 9.2000 -64 E HA 3.4000 -64 E HB2 2.4500 -64 E HB3 2.4699 -64 E HG2 2.3100 -64 E HG3 2.3100 -64 E N 115.5791 -65 S C 171.7815 -65 S CA 60.3000 -65 S CB 64.4000 -65 S H 7.6400 -65 S HA 4.6500 -65 S HB2 3.6965 -65 S HB3 3.9000 -65 S N 113.2143 -66 T C 174.0200 -66 T CA 61.7000 -66 T CB 69.3893 -66 T CG2 21.5000 -66 T H 8.6100 -66 T HA 5.3200 -66 T HB 4.0669 -66 T HG2 0.9678 -66 T N 120.3186 -67 L C 175.5200 -67 L CA 53.9000 -67 L CB 43.0971 -67 L CD1 25.3000 -67 L CD2 23.6000 -67 L CG 27.4791 -67 L H 9.3600 -67 L HA 5.0800 -67 L HB2 1.4900 -67 L HB3 1.6455 -67 L HD1 0.6900 -67 L HD2 0.7030 -67 L HG 1.6974 -67 L N 124.9410 -68 H C 173.4200 -68 H CA 54.7000 -68 H CB 30.3527 -68 H CD2 119.8119 -68 H CE1 136.5591 -68 H CG 132.4871 -68 H H 9.1900 -68 H HA 5.2100 -68 H HB2 2.9600 -68 H HB3 2.9621 -68 H HD2 7.0318 -68 H HE1 8.3400 -68 H N 118.4800 -69 L C 175.2200 -69 L CA 54.0000 -69 L CB 43.9000 -69 L CD1 24.4945 -69 L CD2 25.1194 -69 L CG 27.6296 -69 L H 8.3000 -69 L HA 5.1900 -69 L HB2 1.3122 -69 L HB3 1.5024 -69 L HD1 0.7600 -69 L HD2 0.8800 -69 L HG 1.3700 -69 L N 125.4800 -70 V C 174.1575 -70 V CA 60.4000 -70 V CB 35.1000 -70 V CG1 21.7000 -70 V CG2 20.9000 -70 V H 9.1300 -70 V HA 4.3600 -70 V HB 2.0500 -70 V HG1 0.8700 -70 V HG2 0.9500 -70 V N 126.5800 -71 L C 176.5840 -71 L CA 54.0969 -71 L CB 42.8394 -71 L CD1 25.1512 -71 L CD2 24.3450 -71 L CG 27.1176 -71 L H 7.9846 -71 L HA 5.0700 -71 L HB2 1.5900 -71 L HB3 1.5599 -71 L HD1 0.8800 -71 L HD2 0.9637 -71 L HG 1.6900 -71 L N 127.1015 -72 R C 175.3998 -72 R CA 54.8381 -72 R CB 31.4356 -72 R CD 43.3561 -72 R CG 26.9092 -72 R CZ 159.7666 -72 R H 8.5300 -72 R HA 4.2900 -72 R HB2 1.5938 -72 R HB3 1.7800 -72 R HD2 3.1900 -72 R HD3 3.1900 -72 R HE 7.1253 -72 R HG2 1.5300 -72 R HG3 1.5399 -72 R N 122.0705 -73 L C 176.5792 -73 L CA 55.9781 -73 L CB 42.4321 -73 L CD1 24.6472 -73 L CD2 24.0535 -73 L CG 27.1240 -73 L H 8.1500 -73 L HA 4.4100 -73 L HB2 1.6500 -73 L HB3 1.6500 -73 L HD1 0.8900 -73 L HD2 0.9400 -73 L HG 1.6300 -73 L N 125.1707 -74 R C 175.8516 -74 R CA 55.4175 -74 R CB 30.5944 -74 R CD 43.3332 -74 R CG 27.2423 -74 R CZ 159.6895 -74 R H 8.2500 -74 R HA 4.3200 -74 R HB2 1.8000 -74 R HB3 1.8900 -74 R HD2 3.2200 -74 R HD3 3.2200 -74 R HE 7.2200 -74 R HG2 1.6500 -74 R HG3 1.6500 -74 R N 120.3350 -75 G C 174.2464 -75 G CA 45.0469 -75 G H 8.3200 -75 G HA 3.9651 -75 G HA2 3.9700 -75 G HA3 3.9509 -75 G N 111.0662 -76 G C 175.5927 -76 G CA 45.8723 -76 G H 7.9253 -76 G HA 3.9321 -76 G HA2 3.7746 -76 G HA3 3.8200 -76 G N 113.9862 diff --git a/example/1ubq-seq.txt b/example/1ubq-seq.txt deleted file mode 100644 index 74ff01b..0000000 --- a/example/1ubq-seq.txt +++ /dev/null @@ -1 +0,0 @@ -MQIFVKTLTGKTITLEVEP SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG diff --git a/example/1ubq.pdb b/example/1ubq.pdb deleted file mode 100644 index 22911b8..0000000 --- a/example/1ubq.pdb +++ /dev/null @@ -1,983 +0,0 @@ -HEADER CHROMOSOMAL PROTEIN 02-JAN-87 1UBQ -TITLE STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION -COMPND MOL_ID: 1; -COMPND 2 MOLECULE: UBIQUITIN; -COMPND 3 CHAIN: A; -COMPND 4 ENGINEERED: YES -SOURCE MOL_ID: 1; -SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; -SOURCE 3 ORGANISM_COMMON: HUMAN; -SOURCE 4 ORGANISM_TAXID: 9606 -KEYWDS CHROMOSOMAL PROTEIN -EXPDTA X-RAY DIFFRACTION -AUTHOR S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK -REVDAT 4 24-FEB-09 1UBQ 1 VERSN -REVDAT 3 01-APR-03 1UBQ 1 JRNL -REVDAT 2 16-JUL-87 1UBQ 1 JRNL REMARK -REVDAT 1 16-APR-87 1UBQ 0 -JRNL AUTH S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK -JRNL TITL STRUCTURE OF UBIQUITIN REFINED AT 1.8 A RESOLUTION. -JRNL REF J.MOL.BIOL. V. 194 531 1987 -JRNL REFN ISSN 0022-2836 -JRNL PMID 3041007 -JRNL DOI 10.1016/0022-2836(87)90679-6 -REMARK 1 -REMARK 1 REFERENCE 1 -REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,R.D.VIERSTRA, -REMARK 1 AUTH 2 P.M.HATFIELD,W.J.COOK -REMARK 1 TITL COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF -REMARK 1 TITL 2 HUMAN, YEAST, AND OAT UBIQUITIN -REMARK 1 REF J.BIOL.CHEM. V. 262 6396 1987 -REMARK 1 REFN ISSN 0021-9258 -REMARK 1 REFERENCE 2 -REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,W.J.COOK -REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF UBIQUITIN AT 2.8 -REMARK 1 TITL 2 ANGSTROMS RESOLUTION -REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 3582 1985 -REMARK 1 REFN ISSN 0027-8424 -REMARK 1 REFERENCE 3 -REMARK 1 AUTH W.J.COOK,F.L.SUDDATH,C.E.BUGG,G.GOLDSTEIN -REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY -REMARK 1 TITL 2 INVESTIGATION OF UBIQUITIN, A NON-HISTONE -REMARK 1 TITL 3 CHROMOSOMAL PROTEIN -REMARK 1 REF J.MOL.BIOL. V. 130 353 1979 -REMARK 1 REFN ISSN 0022-2836 -REMARK 1 REFERENCE 4 -REMARK 1 AUTH D.H.SCHLESINGER,G.GOLDSTEIN -REMARK 1 TITL MOLECULAR CONSERVATION OF 74 AMINO ACID SEQUENCE -REMARK 1 TITL 2 OF UBIQUITIN BETWEEN CATTLE AND MAN -REMARK 1 REF NATURE V. 255 423 1975 -REMARK 1 REFN ISSN 0028-0836 -REMARK 2 -REMARK 2 RESOLUTION. 1.80 ANGSTROMS. -REMARK 3 -REMARK 3 REFINEMENT. -REMARK 3 PROGRAM : PROLSQ -REMARK 3 AUTHORS : KONNERT,HENDRICKSON -REMARK 3 -REMARK 3 DATA USED IN REFINEMENT. -REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 -REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL -REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL -REMARK 3 COMPLETENESS FOR RANGE (%) : NULL -REMARK 3 NUMBER OF REFLECTIONS : NULL -REMARK 3 -REMARK 3 FIT TO DATA USED IN REFINEMENT. -REMARK 3 CROSS-VALIDATION METHOD : NULL -REMARK 3 FREE R VALUE TEST SET SELECTION : NULL -REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 -REMARK 3 R VALUE (WORKING SET) : NULL -REMARK 3 FREE R VALUE : NULL -REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL -REMARK 3 FREE R VALUE TEST SET COUNT : NULL -REMARK 3 -REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. -REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL -REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL -REMARK 3 FREE R VALUE (NO CUTOFF) : NULL -REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL -REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL -REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL -REMARK 3 -REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. -REMARK 3 PROTEIN ATOMS : 602 -REMARK 3 NUCLEIC ACID ATOMS : 0 -REMARK 3 HETEROGEN ATOMS : 0 -REMARK 3 SOLVENT ATOMS : 58 -REMARK 3 -REMARK 3 B VALUES. -REMARK 3 FROM WILSON PLOT (A**2) : NULL -REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL -REMARK 3 OVERALL ANISOTROPIC B VALUE. -REMARK 3 B11 (A**2) : NULL -REMARK 3 B22 (A**2) : NULL -REMARK 3 B33 (A**2) : NULL -REMARK 3 B12 (A**2) : NULL -REMARK 3 B13 (A**2) : NULL -REMARK 3 B23 (A**2) : NULL -REMARK 3 -REMARK 3 ESTIMATED COORDINATE ERROR. -REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL -REMARK 3 ESD FROM SIGMAA (A) : NULL -REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL -REMARK 3 -REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. -REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA -REMARK 3 BOND LENGTH (A) : 0.016 ; NULL -REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL -REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL -REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL -REMARK 3 -REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL -REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL -REMARK 3 -REMARK 3 NON-BONDED CONTACT RESTRAINTS. -REMARK 3 SINGLE TORSION (A) : NULL ; NULL -REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL -REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL -REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL -REMARK 3 -REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. -REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL -REMARK 3 PLANAR (DEGREES) : NULL ; NULL -REMARK 3 STAGGERED (DEGREES) : NULL ; NULL -REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL -REMARK 3 -REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA -REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL -REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL -REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL -REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL -REMARK 3 -REMARK 3 OTHER REFINEMENT REMARKS: NULL -REMARK 4 -REMARK 4 1UBQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 -REMARK 100 -REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. -REMARK 200 -REMARK 200 EXPERIMENTAL DETAILS -REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION -REMARK 200 DATE OF DATA COLLECTION : NULL -REMARK 200 TEMPERATURE (KELVIN) : NULL -REMARK 200 PH : NULL -REMARK 200 NUMBER OF CRYSTALS USED : NULL -REMARK 200 -REMARK 200 SYNCHROTRON (Y/N) : NULL -REMARK 200 RADIATION SOURCE : NULL -REMARK 200 BEAMLINE : NULL -REMARK 200 X-RAY GENERATOR MODEL : NULL -REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL -REMARK 200 WAVELENGTH OR RANGE (A) : NULL -REMARK 200 MONOCHROMATOR : NULL -REMARK 200 OPTICS : NULL -REMARK 200 -REMARK 200 DETECTOR TYPE : NULL -REMARK 200 DETECTOR MANUFACTURER : NULL -REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL -REMARK 200 DATA SCALING SOFTWARE : NULL -REMARK 200 -REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL -REMARK 200 RESOLUTION RANGE HIGH (A) : NULL -REMARK 200 RESOLUTION RANGE LOW (A) : NULL -REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL -REMARK 200 -REMARK 200 OVERALL. -REMARK 200 COMPLETENESS FOR RANGE (%) : NULL -REMARK 200 DATA REDUNDANCY : NULL -REMARK 200 R MERGE (I) : NULL -REMARK 200 R SYM (I) : NULL -REMARK 200 FOR THE DATA SET : NULL -REMARK 200 -REMARK 200 IN THE HIGHEST RESOLUTION SHELL. -REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL -REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL -REMARK 200 COMPLETENESS FOR SHELL (%) : NULL -REMARK 200 DATA REDUNDANCY IN SHELL : NULL -REMARK 200 R MERGE FOR SHELL (I) : NULL -REMARK 200 R SYM FOR SHELL (I) : NULL -REMARK 200 FOR SHELL : NULL -REMARK 200 -REMARK 200 DIFFRACTION PROTOCOL: NULL -REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL -REMARK 200 SOFTWARE USED: NULL -REMARK 200 STARTING MODEL: NULL -REMARK 200 -REMARK 200 REMARK: NULL -REMARK 280 -REMARK 280 CRYSTAL -REMARK 280 SOLVENT CONTENT, VS (%): 32.94 -REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 -REMARK 280 -REMARK 280 CRYSTALLIZATION CONDITIONS: NULL -REMARK 290 -REMARK 290 CRYSTALLOGRAPHIC SYMMETRY -REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 -REMARK 290 -REMARK 290 SYMOP SYMMETRY -REMARK 290 NNNMMM OPERATOR -REMARK 290 1555 X,Y,Z -REMARK 290 2555 -X+1/2,-Y,Z+1/2 -REMARK 290 3555 -X,Y+1/2,-Z+1/2 -REMARK 290 4555 X+1/2,-Y+1/2,-Z -REMARK 290 -REMARK 290 WHERE NNN -> OPERATOR NUMBER -REMARK 290 MMM -> TRANSLATION VECTOR -REMARK 290 -REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS -REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM -REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY -REMARK 290 RELATED MOLECULES. -REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.42000 -REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.47500 -REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.38500 -REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.47500 -REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42000 -REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.38500 -REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 -REMARK 290 REMARK: NULL -REMARK 300 -REMARK 300 BIOMOLECULE: 1 -REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM -REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN -REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON -REMARK 300 BURIED SURFACE AREA. -REMARK 350 -REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN -REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE -REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS -REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND -REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. -REMARK 350 -REMARK 350 BIOMOLECULE: 1 -REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC -REMARK 350 APPLY THE FOLLOWING TO CHAINS: A -REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 -REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 -REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: CLOSE CONTACTS -REMARK 500 -REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC -REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 -REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A -REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 -REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE -REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. -REMARK 500 -REMARK 500 DISTANCE CUTOFF: -REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS -REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS -REMARK 500 -REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE -REMARK 500 OE2 GLU A 16 NH1 ARG A 72 1554 2.02 -REMARK 500 NZ LYS A 48 OXT GLY A 76 4467 2.16 -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: COVALENT BOND ANGLES -REMARK 500 -REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES -REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE -REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN -REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). -REMARK 500 -REMARK 500 STANDARD TABLE: -REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) -REMARK 500 -REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 -REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 -REMARK 500 -REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 -REMARK 500 LEU A 15 CA - CB - CG ANGL. DEV. = 14.0 DEGREES -REMARK 500 ARG A 54 CD - NE - CZ ANGL. DEV. = 12.4 DEGREES -REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 525 -REMARK 525 SOLVENT -REMARK 525 -REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT -REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST -REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT -REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE -REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; -REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE -REMARK 525 NUMBER; I=INSERTION CODE): -REMARK 525 -REMARK 525 M RES CSSEQI -REMARK 525 HOH A 93 DISTANCE = 5.65 ANGSTROMS -REMARK 525 HOH A 114 DISTANCE = 5.45 ANGSTROMS -REMARK 525 HOH A 126 DISTANCE = 5.71 ANGSTROMS -DBREF 1UBQ A 1 76 UNP P62988 UBIQ_HUMAN 1 76 -SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE -SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL -SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP -SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP -SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER -SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY -FORMUL 2 HOH *58(H2 O) -HELIX 1 H1 ILE A 23 GLU A 34 1 12 -HELIX 2 H2 LEU A 56 TYR A 59 5 4 -SHEET 1 BET 5 GLY A 10 VAL A 17 0 -SHEET 2 BET 5 MET A 1 THR A 7 -1 -SHEET 3 BET 5 GLU A 64 ARG A 72 1 -SHEET 4 BET 5 GLN A 40 PHE A 45 -1 -SHEET 5 BET 5 LYS A 48 LEU A 50 -1 -CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 4 -ORIGX1 1.000000 0.000000 0.000000 0.00000 -ORIGX2 0.000000 1.000000 0.000000 0.00000 -ORIGX3 0.000000 0.000000 1.000000 0.00000 -SCALE1 0.019670 0.000000 0.000000 0.00000 -SCALE2 0.000000 0.023381 0.000000 0.00000 -SCALE3 0.000000 0.000000 0.034542 0.00000 -ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 9.67 N -ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 10.38 C -ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 9.62 C -ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 9.62 O -ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 13.77 C -ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 16.29 C -ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 17.17 S -ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 16.11 C -ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 9.27 N -ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 9.07 C -ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 8.72 C -ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 8.22 O -ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 14.46 C -ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 17.01 C -ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 20.10 C -ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 21.89 O -ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 19.49 N -ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 5.87 N -ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 5.07 C -ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 4.01 C -ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 4.61 O -ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 6.55 C -ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 4.72 C -ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 5.58 C -ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 10.83 C -ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 4.55 N -ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 4.68 C -ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 5.30 C -ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 5.58 O -ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 4.83 C -ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 7.97 C -ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 6.69 C -ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 8.34 C -ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 9.10 C -ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 10.61 C -ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 8.90 C -ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N -ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C -ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C -ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O -ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C -ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 5.28 C -ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 9.13 C -ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 6.04 N -ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 6.12 C -ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 6.57 C -ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 5.76 O -ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 7.45 C -ATOM 49 CG LYS A 6 25.884 39.139 14.615 1.00 11.12 C -ATOM 50 CD LYS A 6 24.348 39.296 14.642 1.00 14.54 C -ATOM 51 CE LYS A 6 23.865 40.723 14.749 1.00 18.84 C -ATOM 52 NZ LYS A 6 22.375 40.720 14.907 1.00 20.55 N -ATOM 53 N THR A 7 29.426 38.430 15.446 1.00 7.41 N -ATOM 54 CA THR A 7 30.225 38.643 16.662 1.00 7.48 C -ATOM 55 C THR A 7 29.664 39.839 17.434 1.00 8.75 C -ATOM 56 O THR A 7 28.850 40.565 16.859 1.00 8.58 O -ATOM 57 CB THR A 7 31.744 38.879 16.299 1.00 9.61 C -ATOM 58 OG1 THR A 7 31.737 40.257 15.824 1.00 11.78 O -ATOM 59 CG2 THR A 7 32.260 37.969 15.171 1.00 9.17 C -ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 9.84 N -ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 14.15 C -ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 17.37 C -ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 17.01 O -ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 16.63 C -ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 18.88 C -ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 19.31 C -ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 18.59 C -ATOM 68 N THR A 9 30.991 42.571 17.998 1.00 18.33 N -ATOM 69 CA THR A 9 31.422 43.940 17.553 1.00 19.24 C -ATOM 70 C THR A 9 30.755 44.351 16.277 1.00 19.48 C -ATOM 71 O THR A 9 31.207 45.268 15.566 1.00 23.14 O -ATOM 72 CB THR A 9 32.979 43.918 17.445 1.00 18.97 C -ATOM 73 OG1 THR A 9 33.174 43.067 16.265 1.00 20.24 O -ATOM 74 CG2 THR A 9 33.657 43.319 18.672 1.00 19.70 C -ATOM 75 N GLY A 10 29.721 43.673 15.885 1.00 19.43 N -ATOM 76 CA GLY A 10 28.978 43.960 14.678 1.00 18.74 C -ATOM 77 C GLY A 10 29.604 43.507 13.393 1.00 17.62 C -ATOM 78 O GLY A 10 29.219 43.981 12.301 1.00 19.74 O -ATOM 79 N LYS A 11 30.563 42.623 13.495 1.00 13.56 N -ATOM 80 CA LYS A 11 31.191 42.012 12.331 1.00 11.91 C -ATOM 81 C LYS A 11 30.459 40.666 12.130 1.00 10.18 C -ATOM 82 O LYS A 11 30.253 39.991 13.133 1.00 9.10 O -ATOM 83 CB LYS A 11 32.672 41.717 12.505 1.00 13.43 C -ATOM 84 CG LYS A 11 33.280 41.086 11.227 1.00 16.69 C -ATOM 85 CD LYS A 11 34.762 40.799 11.470 1.00 17.92 C -ATOM 86 CE LYS A 11 35.614 40.847 10.240 1.00 20.81 C -ATOM 87 NZ LYS A 11 35.100 40.073 9.101 1.00 21.93 N -ATOM 88 N THR A 12 30.163 40.338 10.886 1.00 9.63 N -ATOM 89 CA THR A 12 29.542 39.020 10.653 1.00 9.85 C -ATOM 90 C THR A 12 30.494 38.261 9.729 1.00 11.66 C -ATOM 91 O THR A 12 30.849 38.850 8.706 1.00 12.33 O -ATOM 92 CB THR A 12 28.113 39.049 10.015 1.00 10.85 C -ATOM 93 OG1 THR A 12 27.280 39.722 10.996 1.00 10.91 O -ATOM 94 CG2 THR A 12 27.588 37.635 9.715 1.00 9.63 C -ATOM 95 N ILE A 13 30.795 37.015 10.095 1.00 10.42 N -ATOM 96 CA ILE A 13 31.720 36.289 9.176 1.00 11.84 C -ATOM 97 C ILE A 13 30.955 35.211 8.459 1.00 10.55 C -ATOM 98 O ILE A 13 30.025 34.618 9.040 1.00 11.92 O -ATOM 99 CB ILE A 13 32.995 35.883 9.934 1.00 14.86 C -ATOM 100 CG1 ILE A 13 33.306 34.381 9.840 1.00 14.87 C -ATOM 101 CG2 ILE A 13 33.109 36.381 11.435 1.00 17.08 C -ATOM 102 CD1 ILE A 13 34.535 34.028 10.720 1.00 16.46 C -ATOM 103 N THR A 14 31.244 34.986 7.197 1.00 9.39 N -ATOM 104 CA THR A 14 30.505 33.884 6.512 1.00 9.63 C -ATOM 105 C THR A 14 31.409 32.680 6.446 1.00 11.20 C -ATOM 106 O THR A 14 32.619 32.812 6.125 1.00 11.63 O -ATOM 107 CB THR A 14 30.091 34.393 5.078 1.00 10.38 C -ATOM 108 OG1 THR A 14 31.440 34.513 4.487 1.00 16.30 O -ATOM 109 CG2 THR A 14 29.420 35.756 5.119 1.00 11.66 C -ATOM 110 N LEU A 15 30.884 31.485 6.666 1.00 8.29 N -ATOM 111 CA LEU A 15 31.677 30.275 6.639 1.00 9.03 C -ATOM 112 C LEU A 15 31.022 29.288 5.665 1.00 8.59 C -ATOM 113 O LEU A 15 29.809 29.395 5.545 1.00 7.79 O -ATOM 114 CB LEU A 15 31.562 29.686 8.045 1.00 11.08 C -ATOM 115 CG LEU A 15 32.631 29.444 9.060 1.00 15.79 C -ATOM 116 CD1 LEU A 15 33.814 30.390 9.030 1.00 15.88 C -ATOM 117 CD2 LEU A 15 31.945 29.449 10.436 1.00 15.27 C -ATOM 118 N GLU A 16 31.834 28.412 5.125 1.00 11.04 N -ATOM 119 CA GLU A 16 31.220 27.341 4.275 1.00 11.50 C -ATOM 120 C GLU A 16 31.440 26.079 5.080 1.00 10.13 C -ATOM 121 O GLU A 16 32.576 25.802 5.461 1.00 9.83 O -ATOM 122 CB GLU A 16 31.827 27.262 2.894 1.00 17.22 C -ATOM 123 CG GLU A 16 31.363 28.410 1.962 1.00 23.33 C -ATOM 124 CD GLU A 16 31.671 28.291 0.498 1.00 26.99 C -ATOM 125 OE1 GLU A 16 30.869 28.621 -0.366 1.00 28.86 O -ATOM 126 OE2 GLU A 16 32.835 27.861 0.278 1.00 28.90 O -ATOM 127 N VAL A 17 30.310 25.458 5.384 1.00 8.99 N -ATOM 128 CA VAL A 17 30.288 24.245 6.193 1.00 8.85 C -ATOM 129 C VAL A 17 29.279 23.227 5.641 1.00 8.04 C -ATOM 130 O VAL A 17 28.478 23.522 4.725 1.00 8.99 O -ATOM 131 CB VAL A 17 29.903 24.590 7.665 1.00 9.78 C -ATOM 132 CG1 VAL A 17 30.862 25.496 8.389 1.00 12.05 C -ATOM 133 CG2 VAL A 17 28.476 25.135 7.705 1.00 10.54 C -ATOM 134 N GLU A 18 29.380 22.057 6.232 1.00 7.29 N -ATOM 135 CA GLU A 18 28.468 20.940 5.980 1.00 7.08 C -ATOM 136 C GLU A 18 27.819 20.609 7.316 1.00 6.45 C -ATOM 137 O GLU A 18 28.449 20.674 8.360 1.00 5.28 O -ATOM 138 CB GLU A 18 29.213 19.697 5.506 1.00 10.28 C -ATOM 139 CG GLU A 18 29.728 19.755 4.060 1.00 12.65 C -ATOM 140 CD GLU A 18 28.754 20.061 2.978 1.00 14.15 C -ATOM 141 OE1 GLU A 18 27.546 19.992 2.985 1.00 14.33 O -ATOM 142 OE2 GLU A 18 29.336 20.423 1.904 1.00 18.17 O -ATOM 143 N PRO A 19 26.559 20.220 7.288 1.00 7.24 N -ATOM 144 CA PRO A 19 25.829 19.825 8.494 1.00 7.07 C -ATOM 145 C PRO A 19 26.541 18.732 9.251 1.00 6.65 C -ATOM 146 O PRO A 19 26.333 18.536 10.457 1.00 6.37 O -ATOM 147 CB PRO A 19 24.469 19.332 7.952 1.00 7.61 C -ATOM 148 CG PRO A 19 24.299 20.134 6.704 1.00 8.16 C -ATOM 149 CD PRO A 19 25.714 20.108 6.073 1.00 7.49 C -ATOM 150 N SER A 20 27.361 17.959 8.559 1.00 6.80 N -ATOM 151 CA SER A 20 28.054 16.835 9.210 1.00 6.28 C -ATOM 152 C SER A 20 29.258 17.318 9.984 1.00 8.45 C -ATOM 153 O SER A 20 29.930 16.477 10.606 1.00 7.26 O -ATOM 154 CB SER A 20 28.523 15.820 8.182 1.00 8.57 C -ATOM 155 OG SER A 20 28.946 16.445 6.967 1.00 11.13 O -ATOM 156 N ASP A 21 29.599 18.599 9.828 1.00 7.50 N -ATOM 157 CA ASP A 21 30.796 19.083 10.566 1.00 7.70 C -ATOM 158 C ASP A 21 30.491 19.162 12.040 1.00 7.08 C -ATOM 159 O ASP A 21 29.367 19.523 12.441 1.00 8.11 O -ATOM 160 CB ASP A 21 31.155 20.515 10.048 1.00 11.00 C -ATOM 161 CG ASP A 21 31.923 20.436 8.755 1.00 15.32 C -ATOM 162 OD1 ASP A 21 32.493 19.374 8.456 1.00 18.03 O -ATOM 163 OD2 ASP A 21 31.838 21.402 7.968 1.00 14.36 O -ATOM 164 N THR A 22 31.510 18.936 12.852 1.00 5.37 N -ATOM 165 CA THR A 22 31.398 19.064 14.286 1.00 6.01 C -ATOM 166 C THR A 22 31.593 20.553 14.655 1.00 8.01 C -ATOM 167 O THR A 22 32.159 21.311 13.861 1.00 8.11 O -ATOM 168 CB THR A 22 32.492 18.193 14.995 1.00 8.92 C -ATOM 169 OG1 THR A 22 33.778 18.739 14.516 1.00 10.22 O -ATOM 170 CG2 THR A 22 32.352 16.700 14.630 1.00 9.65 C -ATOM 171 N ILE A 23 31.113 20.863 15.860 1.00 8.32 N -ATOM 172 CA ILE A 23 31.288 22.201 16.417 1.00 9.92 C -ATOM 173 C ILE A 23 32.776 22.519 16.577 1.00 10.01 C -ATOM 174 O ILE A 23 33.233 23.659 16.384 1.00 8.71 O -ATOM 175 CB ILE A 23 30.520 22.300 17.764 1.00 10.78 C -ATOM 176 CG1 ILE A 23 29.006 22.043 17.442 1.00 11.38 C -ATOM 177 CG2 ILE A 23 30.832 23.699 18.358 1.00 10.90 C -ATOM 178 CD1 ILE A 23 28.407 22.948 16.366 1.00 12.30 C -ATOM 179 N GLU A 24 33.548 21.526 16.950 1.00 9.54 N -ATOM 180 CA GLU A 24 35.031 21.722 17.069 1.00 11.81 C -ATOM 181 C GLU A 24 35.615 22.190 15.759 1.00 11.14 C -ATOM 182 O GLU A 24 36.532 23.046 15.724 1.00 10.62 O -ATOM 183 CB GLU A 24 35.667 20.383 17.447 1.00 19.24 C -ATOM 184 CG GLU A 24 37.128 20.293 17.872 1.00 27.76 C -ATOM 185 CD GLU A 24 37.561 18.851 18.082 1.00 32.92 C -ATOM 186 OE1 GLU A 24 37.758 18.024 17.195 1.00 34.80 O -ATOM 187 OE2 GLU A 24 37.628 18.599 19.313 1.00 36.51 O -ATOM 188 N ASN A 25 35.139 21.624 14.662 1.00 9.43 N -ATOM 189 CA ASN A 25 35.590 21.945 13.302 1.00 10.96 C -ATOM 190 C ASN A 25 35.238 23.382 12.920 1.00 9.68 C -ATOM 191 O ASN A 25 36.066 24.109 12.333 1.00 9.33 O -ATOM 192 CB ASN A 25 35.064 20.957 12.255 1.00 16.78 C -ATOM 193 CG ASN A 25 35.541 21.418 10.871 1.00 22.31 C -ATOM 194 OD1 ASN A 25 36.772 21.623 10.676 1.00 25.66 O -ATOM 195 ND2 ASN A 25 34.628 21.595 9.920 1.00 24.70 N -ATOM 196 N VAL A 26 34.007 23.745 13.250 1.00 6.52 N -ATOM 197 CA VAL A 26 33.533 25.097 12.978 1.00 5.53 C -ATOM 198 C VAL A 26 34.441 26.099 13.684 1.00 4.42 C -ATOM 199 O VAL A 26 34.883 27.090 13.093 1.00 3.40 O -ATOM 200 CB VAL A 26 32.060 25.257 13.364 1.00 3.86 C -ATOM 201 CG1 VAL A 26 31.684 26.749 13.342 1.00 7.25 C -ATOM 202 CG2 VAL A 26 31.152 24.421 12.477 1.00 8.12 C -ATOM 203 N LYS A 27 34.734 25.822 14.949 1.00 2.64 N -ATOM 204 CA LYS A 27 35.596 26.715 15.736 1.00 4.14 C -ATOM 205 C LYS A 27 36.975 26.826 15.107 1.00 5.58 C -ATOM 206 O LYS A 27 37.579 27.926 15.159 1.00 4.11 O -ATOM 207 CB LYS A 27 35.715 26.203 17.172 1.00 3.97 C -ATOM 208 CG LYS A 27 34.343 26.445 17.898 1.00 7.45 C -ATOM 209 CD LYS A 27 34.509 26.077 19.360 1.00 9.02 C -ATOM 210 CE LYS A 27 33.206 26.311 20.122 1.00 12.90 C -ATOM 211 NZ LYS A 27 33.455 25.910 21.546 1.00 15.47 N -ATOM 212 N ALA A 28 37.499 25.743 14.571 1.00 6.61 N -ATOM 213 CA ALA A 28 38.794 25.761 13.880 1.00 7.74 C -ATOM 214 C ALA A 28 38.728 26.591 12.611 1.00 9.17 C -ATOM 215 O ALA A 28 39.704 27.346 12.277 1.00 11.45 O -ATOM 216 CB ALA A 28 39.285 24.336 13.566 1.00 7.68 C -ATOM 217 N LYS A 29 37.633 26.543 11.867 1.00 8.96 N -ATOM 218 CA LYS A 29 37.471 27.391 10.668 1.00 7.90 C -ATOM 219 C LYS A 29 37.441 28.882 11.052 1.00 6.92 C -ATOM 220 O LYS A 29 38.020 29.772 10.382 1.00 6.87 O -ATOM 221 CB LYS A 29 36.193 27.058 9.911 1.00 10.28 C -ATOM 222 CG LYS A 29 36.153 25.620 9.409 1.00 14.94 C -ATOM 223 CD LYS A 29 34.758 25.280 8.900 1.00 19.69 C -ATOM 224 CE LYS A 29 34.793 24.264 7.767 1.00 22.63 C -ATOM 225 NZ LYS A 29 34.914 24.944 6.441 1.00 24.98 N -ATOM 226 N ILE A 30 36.811 29.170 12.192 1.00 4.57 N -ATOM 227 CA ILE A 30 36.731 30.570 12.645 1.00 5.58 C -ATOM 228 C ILE A 30 38.148 30.981 13.069 1.00 7.26 C -ATOM 229 O ILE A 30 38.544 32.150 12.856 1.00 9.46 O -ATOM 230 CB ILE A 30 35.708 30.776 13.806 1.00 5.36 C -ATOM 231 CG1 ILE A 30 34.228 30.630 13.319 1.00 2.94 C -ATOM 232 CG2 ILE A 30 35.874 32.138 14.512 1.00 2.78 C -ATOM 233 CD1 ILE A 30 33.284 30.504 14.552 1.00 2.00 C -ATOM 234 N GLN A 31 38.883 30.110 13.713 1.00 7.06 N -ATOM 235 CA GLN A 31 40.269 30.508 14.115 1.00 8.67 C -ATOM 236 C GLN A 31 41.092 30.808 12.851 1.00 10.90 C -ATOM 237 O GLN A 31 41.828 31.808 12.681 1.00 9.63 O -ATOM 238 CB GLN A 31 40.996 29.399 14.865 1.00 9.12 C -ATOM 239 CG GLN A 31 42.445 29.848 15.182 1.00 10.76 C -ATOM 240 CD GLN A 31 43.090 28.828 16.095 1.00 13.78 C -ATOM 241 OE1 GLN A 31 42.770 27.655 15.906 1.00 14.48 O -ATOM 242 NE2 GLN A 31 43.898 29.252 17.050 1.00 14.76 N -ATOM 243 N ASP A 32 41.001 29.878 11.931 1.00 10.93 N -ATOM 244 CA ASP A 32 41.718 30.022 10.643 1.00 14.01 C -ATOM 245 C ASP A 32 41.399 31.338 9.967 1.00 14.04 C -ATOM 246 O ASP A 32 42.260 32.036 9.381 1.00 13.39 O -ATOM 247 CB ASP A 32 41.398 28.780 9.810 1.00 18.01 C -ATOM 248 CG ASP A 32 42.626 28.557 8.928 1.00 24.33 C -ATOM 249 OD1 ASP A 32 43.666 28.262 9.539 1.00 26.29 O -ATOM 250 OD2 ASP A 32 42.430 28.812 7.728 1.00 25.17 O -ATOM 251 N LYS A 33 40.117 31.750 9.988 1.00 14.22 N -ATOM 252 CA LYS A 33 39.808 32.994 9.233 1.00 14.00 C -ATOM 253 C LYS A 33 39.837 34.271 9.995 1.00 12.37 C -ATOM 254 O LYS A 33 40.164 35.323 9.345 1.00 12.17 O -ATOM 255 CB LYS A 33 38.615 32.801 8.320 1.00 18.62 C -ATOM 256 CG LYS A 33 37.220 32.822 8.827 1.00 24.00 C -ATOM 257 CD LYS A 33 36.351 33.613 7.838 1.00 27.61 C -ATOM 258 CE LYS A 33 36.322 32.944 6.477 1.00 27.64 C -ATOM 259 NZ LYS A 33 35.768 33.945 5.489 1.00 30.06 N -ATOM 260 N GLU A 34 39.655 34.335 11.285 1.00 10.11 N -ATOM 261 CA GLU A 34 39.676 35.547 12.072 1.00 10.07 C -ATOM 262 C GLU A 34 40.675 35.527 13.200 1.00 9.32 C -ATOM 263 O GLU A 34 40.814 36.528 13.911 1.00 11.61 O -ATOM 264 CB GLU A 34 38.290 35.814 12.698 1.00 14.77 C -ATOM 265 CG GLU A 34 37.156 35.985 11.688 1.00 18.75 C -ATOM 266 CD GLU A 34 37.192 37.361 11.033 1.00 22.28 C -ATOM 267 OE1 GLU A 34 37.519 38.360 11.645 1.00 21.95 O -ATOM 268 OE2 GLU A 34 36.861 37.320 9.822 1.00 25.19 O -ATOM 269 N GLY A 35 41.317 34.393 13.432 1.00 7.22 N -ATOM 270 CA GLY A 35 42.345 34.269 14.431 1.00 6.29 C -ATOM 271 C GLY A 35 41.949 34.076 15.842 1.00 6.93 C -ATOM 272 O GLY A 35 42.829 34.000 16.739 1.00 7.41 O -ATOM 273 N ILE A 36 40.642 33.916 16.112 1.00 5.86 N -ATOM 274 CA ILE A 36 40.226 33.716 17.509 1.00 6.07 C -ATOM 275 C ILE A 36 40.449 32.278 17.945 1.00 6.36 C -ATOM 276 O ILE A 36 39.936 31.336 17.315 1.00 6.18 O -ATOM 277 CB ILE A 36 38.693 34.106 17.595 1.00 7.47 C -ATOM 278 CG1 ILE A 36 38.471 35.546 17.045 1.00 8.52 C -ATOM 279 CG2 ILE A 36 38.146 33.932 19.027 1.00 7.36 C -ATOM 280 CD1 ILE A 36 36.958 35.746 16.680 1.00 9.49 C -ATOM 281 N PRO A 37 41.189 32.085 19.031 1.00 8.65 N -ATOM 282 CA PRO A 37 41.461 30.751 19.594 1.00 9.18 C -ATOM 283 C PRO A 37 40.168 30.026 19.918 1.00 9.85 C -ATOM 284 O PRO A 37 39.264 30.662 20.521 1.00 8.51 O -ATOM 285 CB PRO A 37 42.195 31.142 20.913 1.00 11.42 C -ATOM 286 CG PRO A 37 42.904 32.414 20.553 1.00 9.27 C -ATOM 287 CD PRO A 37 41.822 33.188 19.813 1.00 8.33 C -ATOM 288 N PRO A 38 40.059 28.758 19.607 1.00 8.71 N -ATOM 289 CA PRO A 38 38.817 28.020 19.889 1.00 9.08 C -ATOM 290 C PRO A 38 38.421 28.048 21.341 1.00 9.28 C -ATOM 291 O PRO A 38 37.213 28.036 21.704 1.00 6.50 O -ATOM 292 CB PRO A 38 39.090 26.629 19.325 1.00 10.31 C -ATOM 293 CG PRO A 38 40.082 26.904 18.198 1.00 10.81 C -ATOM 294 CD PRO A 38 41.035 27.909 18.879 1.00 12.00 C -ATOM 295 N ASP A 39 39.374 28.090 22.240 1.00 11.20 N -ATOM 296 CA ASP A 39 39.063 28.063 23.695 1.00 14.96 C -ATOM 297 C ASP A 39 38.365 29.335 24.159 1.00 13.99 C -ATOM 298 O ASP A 39 37.684 29.390 25.221 1.00 13.75 O -ATOM 299 CB ASP A 39 40.340 27.692 24.468 1.00 24.16 C -ATOM 300 CG ASP A 39 40.559 28.585 25.675 1.00 31.06 C -ATOM 301 OD1 ASP A 39 40.716 29.809 25.456 1.00 35.55 O -ATOM 302 OD2 ASP A 39 40.549 28.090 26.840 1.00 34.22 O -ATOM 303 N GLN A 40 38.419 30.373 23.341 1.00 11.60 N -ATOM 304 CA GLN A 40 37.738 31.637 23.712 1.00 10.76 C -ATOM 305 C GLN A 40 36.334 31.742 23.087 1.00 8.01 C -ATOM 306 O GLN A 40 35.574 32.618 23.483 1.00 8.96 O -ATOM 307 CB GLN A 40 38.528 32.854 23.182 1.00 11.14 C -ATOM 308 CG GLN A 40 39.919 32.854 23.840 1.00 14.85 C -ATOM 309 CD GLN A 40 40.760 34.036 23.394 1.00 16.11 C -ATOM 310 OE1 GLN A 40 41.975 34.008 23.624 1.00 20.52 O -ATOM 311 NE2 GLN A 40 40.140 35.007 22.775 1.00 18.16 N -ATOM 312 N GLN A 41 36.000 30.860 22.172 1.00 6.52 N -ATOM 313 CA GLN A 41 34.738 30.875 21.473 1.00 3.87 C -ATOM 314 C GLN A 41 33.589 30.189 22.181 1.00 4.79 C -ATOM 315 O GLN A 41 33.580 29.009 22.499 1.00 6.34 O -ATOM 316 CB GLN A 41 34.876 30.237 20.066 1.00 4.20 C -ATOM 317 CG GLN A 41 36.012 30.860 19.221 1.00 3.20 C -ATOM 318 CD GLN A 41 36.083 30.194 17.875 1.00 4.89 C -ATOM 319 OE1 GLN A 41 35.048 29.702 17.393 1.00 5.21 O -ATOM 320 NE2 GLN A 41 37.228 30.126 17.233 1.00 7.13 N -ATOM 321 N ARG A 42 32.478 30.917 22.269 1.00 5.73 N -ATOM 322 CA ARG A 42 31.200 30.329 22.780 1.00 6.97 C -ATOM 323 C ARG A 42 30.210 30.509 21.650 1.00 7.15 C -ATOM 324 O ARG A 42 29.978 31.726 21.269 1.00 7.33 O -ATOM 325 CB ARG A 42 30.847 30.931 24.118 1.00 13.23 C -ATOM 326 CG ARG A 42 29.412 30.796 24.598 1.00 21.27 C -ATOM 327 CD ARG A 42 29.271 31.314 26.016 1.00 26.14 C -ATOM 328 NE ARG A 42 27.875 31.317 26.443 1.00 32.26 N -ATOM 329 CZ ARG A 42 27.132 32.423 26.574 1.00 34.32 C -ATOM 330 NH1 ARG A 42 27.630 33.656 26.461 1.00 35.30 N -ATOM 331 NH2 ARG A 42 25.810 32.299 26.732 1.00 36.39 N -ATOM 332 N LEU A 43 29.694 29.436 21.054 1.00 4.65 N -ATOM 333 CA LEU A 43 28.762 29.573 19.906 1.00 3.51 C -ATOM 334 C LEU A 43 27.331 29.317 20.364 1.00 5.56 C -ATOM 335 O LEU A 43 27.101 28.346 21.097 1.00 4.19 O -ATOM 336 CB LEU A 43 29.151 28.655 18.755 1.00 3.74 C -ATOM 337 CG LEU A 43 30.416 28.912 17.980 1.00 6.32 C -ATOM 338 CD1 LEU A 43 30.738 27.693 17.122 1.00 9.55 C -ATOM 339 CD2 LEU A 43 30.205 30.168 17.129 1.00 6.41 C -ATOM 340 N ILE A 44 26.436 30.232 20.004 1.00 4.58 N -ATOM 341 CA ILE A 44 25.034 30.170 20.401 1.00 5.55 C -ATOM 342 C ILE A 44 24.101 30.149 19.196 1.00 5.46 C -ATOM 343 O ILE A 44 24.196 30.948 18.287 1.00 6.04 O -ATOM 344 CB ILE A 44 24.639 31.426 21.286 1.00 6.80 C -ATOM 345 CG1 ILE A 44 25.646 31.670 22.421 1.00 10.31 C -ATOM 346 CG2 ILE A 44 23.181 31.309 21.824 1.00 7.39 C -ATOM 347 CD1 ILE A 44 25.778 30.436 23.356 1.00 13.90 C -ATOM 348 N PHE A 45 23.141 29.187 19.241 1.00 6.75 N -ATOM 349 CA PHE A 45 22.126 29.062 18.183 1.00 4.70 C -ATOM 350 C PHE A 45 20.835 28.629 18.904 1.00 6.34 C -ATOM 351 O PHE A 45 20.821 27.734 19.749 1.00 5.45 O -ATOM 352 CB PHE A 45 22.494 28.057 17.109 1.00 5.51 C -ATOM 353 CG PHE A 45 21.447 27.869 16.026 1.00 5.98 C -ATOM 354 CD1 PHE A 45 21.325 28.813 15.005 1.00 6.86 C -ATOM 355 CD2 PHE A 45 20.638 26.735 16.053 1.00 5.87 C -ATOM 356 CE1 PHE A 45 20.369 28.648 14.001 1.00 6.68 C -ATOM 357 CE2 PHE A 45 19.677 26.539 15.051 1.00 6.64 C -ATOM 358 CZ PHE A 45 19.593 27.465 14.021 1.00 6.84 C -ATOM 359 N ALA A 46 19.810 29.378 18.578 1.00 6.53 N -ATOM 360 CA ALA A 46 18.443 29.143 19.083 1.00 7.15 C -ATOM 361 C ALA A 46 18.453 28.941 20.591 1.00 9.00 C -ATOM 362 O ALA A 46 17.860 27.994 21.128 1.00 11.15 O -ATOM 363 CB ALA A 46 17.864 27.977 18.346 1.00 8.99 C -ATOM 364 N GLY A 47 19.172 29.808 21.243 1.00 9.35 N -ATOM 365 CA GLY A 47 19.399 29.894 22.655 1.00 11.68 C -ATOM 366 C GLY A 47 20.083 28.729 23.321 1.00 11.14 C -ATOM 367 O GLY A 47 19.991 28.584 24.561 1.00 13.93 O -ATOM 368 N LYS A 48 20.801 27.931 22.578 1.00 10.47 N -ATOM 369 CA LYS A 48 21.550 26.796 23.133 1.00 8.82 C -ATOM 370 C LYS A 48 23.046 27.087 22.913 1.00 7.68 C -ATOM 371 O LYS A 48 23.383 27.627 21.870 1.00 6.47 O -ATOM 372 CB LYS A 48 21.242 25.519 22.391 1.00 9.74 C -ATOM 373 CG LYS A 48 19.762 25.077 22.455 1.00 14.14 C -ATOM 374 CD LYS A 48 19.634 23.885 21.531 1.00 16.32 C -ATOM 375 CE LYS A 48 18.791 24.221 20.313 1.00 20.04 C -ATOM 376 NZ LYS A 48 17.440 24.655 20.827 1.00 23.92 N -ATOM 377 N GLN A 49 23.880 26.727 23.851 1.00 8.89 N -ATOM 378 CA GLN A 49 25.349 26.872 23.643 1.00 7.18 C -ATOM 379 C GLN A 49 25.743 25.586 22.922 1.00 8.23 C -ATOM 380 O GLN A 49 25.325 24.489 23.378 1.00 9.70 O -ATOM 381 CB GLN A 49 26.070 27.025 24.960 1.00 11.67 C -ATOM 382 CG GLN A 49 27.553 27.356 24.695 1.00 15.82 C -ATOM 383 CD GLN A 49 28.262 27.576 26.020 1.00 20.21 C -ATOM 384 OE1 GLN A 49 29.189 26.840 26.335 1.00 23.23 O -ATOM 385 NE2 GLN A 49 27.777 28.585 26.739 1.00 20.67 N -ATOM 386 N LEU A 50 26.465 25.689 21.833 1.00 6.51 N -ATOM 387 CA LEU A 50 26.826 24.521 21.012 1.00 7.41 C -ATOM 388 C LEU A 50 27.994 23.781 21.643 1.00 8.27 C -ATOM 389 O LEU A 50 28.904 24.444 22.098 1.00 8.34 O -ATOM 390 CB LEU A 50 27.043 24.992 19.571 1.00 7.13 C -ATOM 391 CG LEU A 50 25.931 25.844 18.959 1.00 7.53 C -ATOM 392 CD1 LEU A 50 26.203 26.083 17.471 1.00 8.14 C -ATOM 393 CD2 LEU A 50 24.577 25.190 19.079 1.00 9.11 C -ATOM 394 N GLU A 51 27.942 22.448 21.648 1.00 9.43 N -ATOM 395 CA GLU A 51 29.015 21.657 22.288 1.00 11.90 C -ATOM 396 C GLU A 51 29.942 21.106 21.240 1.00 11.49 C -ATOM 397 O GLU A 51 29.470 20.677 20.190 1.00 9.88 O -ATOM 398 CB GLU A 51 28.348 20.540 23.066 1.00 16.56 C -ATOM 399 CG GLU A 51 29.247 19.456 23.705 1.00 26.06 C -ATOM 400 CD GLU A 51 28.722 19.047 25.066 1.00 29.86 C -ATOM 401 OE1 GLU A 51 29.139 18.132 25.746 1.00 32.13 O -ATOM 402 OE2 GLU A 51 27.777 19.842 25.367 1.00 33.44 O -ATOM 403 N ASP A 52 31.233 21.090 21.459 1.00 12.71 N -ATOM 404 CA ASP A 52 32.262 20.670 20.514 1.00 16.56 C -ATOM 405 C ASP A 52 32.128 19.364 19.750 1.00 15.83 C -ATOM 406 O ASP A 52 32.546 19.317 18.558 1.00 17.21 O -ATOM 407 CB ASP A 52 33.638 20.716 21.242 1.00 21.05 C -ATOM 408 CG ASP A 52 34.174 22.129 21.354 1.00 25.12 C -ATOM 409 OD1 ASP A 52 35.252 22.322 21.958 1.00 28.37 O -ATOM 410 OD2 ASP A 52 33.544 23.086 20.883 1.00 25.82 O -ATOM 411 N GLY A 53 31.697 18.311 20.406 1.00 15.00 N -ATOM 412 CA GLY A 53 31.568 16.962 19.825 1.00 11.77 C -ATOM 413 C GLY A 53 30.320 16.698 19.051 1.00 11.10 C -ATOM 414 O GLY A 53 30.198 15.657 18.366 1.00 11.25 O -ATOM 415 N ARG A 54 29.340 17.594 19.076 1.00 8.53 N -ATOM 416 CA ARG A 54 28.108 17.439 18.276 1.00 9.05 C -ATOM 417 C ARG A 54 28.375 17.999 16.887 1.00 8.96 C -ATOM 418 O ARG A 54 29.326 18.786 16.690 1.00 11.60 O -ATOM 419 CB ARG A 54 26.926 18.191 18.892 1.00 7.97 C -ATOM 420 CG ARG A 54 26.621 17.799 20.352 1.00 9.62 C -ATOM 421 CD ARG A 54 26.010 16.370 20.280 1.00 12.20 C -ATOM 422 NE ARG A 54 26.975 15.521 20.942 1.00 18.23 N -ATOM 423 CZ ARG A 54 27.603 14.423 20.655 1.00 22.08 C -ATOM 424 NH1 ARG A 54 27.479 13.733 19.537 1.00 23.38 N -ATOM 425 NH2 ARG A 54 28.519 13.967 21.550 1.00 25.50 N -ATOM 426 N THR A 55 27.510 17.689 15.954 1.00 9.05 N -ATOM 427 CA THR A 55 27.574 18.192 14.563 1.00 9.03 C -ATOM 428 C THR A 55 26.482 19.280 14.432 1.00 8.15 C -ATOM 429 O THR A 55 25.609 19.388 15.287 1.00 5.91 O -ATOM 430 CB THR A 55 27.299 17.055 13.533 1.00 11.15 C -ATOM 431 OG1 THR A 55 25.925 16.611 13.913 1.00 11.95 O -ATOM 432 CG2 THR A 55 28.236 15.864 13.558 1.00 11.71 C -ATOM 433 N LEU A 56 26.585 20.063 13.378 1.00 6.91 N -ATOM 434 CA LEU A 56 25.594 21.109 13.072 1.00 8.29 C -ATOM 435 C LEU A 56 24.241 20.436 12.857 1.00 8.05 C -ATOM 436 O LEU A 56 23.264 20.951 13.329 1.00 10.17 O -ATOM 437 CB LEU A 56 26.084 21.888 11.833 1.00 6.60 C -ATOM 438 CG LEU A 56 27.426 22.616 11.902 1.00 7.73 C -ATOM 439 CD1 LEU A 56 27.718 23.341 10.578 1.00 9.85 C -ATOM 440 CD2 LEU A 56 27.380 23.721 12.955 1.00 8.64 C -ATOM 441 N SER A 57 24.240 19.233 12.246 1.00 8.92 N -ATOM 442 CA SER A 57 22.924 18.583 12.025 1.00 9.00 C -ATOM 443 C SER A 57 22.229 18.244 13.325 1.00 9.44 C -ATOM 444 O SER A 57 20.963 18.253 13.395 1.00 10.91 O -ATOM 445 CB SER A 57 23.059 17.326 11.154 1.00 10.32 C -ATOM 446 OG SER A 57 23.914 16.395 11.755 1.00 13.59 O -ATOM 447 N ASP A 58 22.997 17.978 14.366 1.00 9.11 N -ATOM 448 CA ASP A 58 22.418 17.638 15.693 1.00 7.91 C -ATOM 449 C ASP A 58 21.460 18.737 16.163 1.00 9.12 C -ATOM 450 O ASP A 58 20.497 18.506 16.900 1.00 8.61 O -ATOM 451 CB ASP A 58 23.461 17.331 16.741 1.00 8.41 C -ATOM 452 CG ASP A 58 24.184 16.016 16.619 1.00 11.50 C -ATOM 453 OD1 ASP A 58 25.303 15.894 17.152 1.00 10.05 O -ATOM 454 OD2 ASP A 58 23.572 15.107 15.975 1.00 11.70 O -ATOM 455 N TYR A 59 21.846 19.954 15.905 1.00 7.97 N -ATOM 456 CA TYR A 59 21.079 21.149 16.251 1.00 8.45 C -ATOM 457 C TYR A 59 20.142 21.590 15.149 1.00 10.98 C -ATOM 458 O TYR A 59 19.499 22.645 15.321 1.00 12.95 O -ATOM 459 CB TYR A 59 22.085 22.254 16.581 1.00 7.94 C -ATOM 460 CG TYR A 59 22.945 21.951 17.785 1.00 6.91 C -ATOM 461 CD1 TYR A 59 24.272 21.544 17.644 1.00 4.59 C -ATOM 462 CD2 TYR A 59 22.437 22.157 19.065 1.00 6.98 C -ATOM 463 CE1 TYR A 59 25.052 21.285 18.776 1.00 5.39 C -ATOM 464 CE2 TYR A 59 23.204 21.907 20.192 1.00 6.52 C -ATOM 465 CZ TYR A 59 24.517 21.470 20.030 1.00 6.76 C -ATOM 466 OH TYR A 59 25.248 21.302 21.191 1.00 7.63 O -ATOM 467 N ASN A 60 19.993 20.884 14.049 1.00 12.38 N -ATOM 468 CA ASN A 60 19.065 21.352 12.999 1.00 13.94 C -ATOM 469 C ASN A 60 19.442 22.745 12.510 1.00 14.16 C -ATOM 470 O ASN A 60 18.571 23.610 12.289 1.00 14.26 O -ATOM 471 CB ASN A 60 17.586 21.282 13.461 1.00 19.23 C -ATOM 472 CG ASN A 60 16.576 21.258 12.315 1.00 22.65 C -ATOM 473 OD1 ASN A 60 15.440 21.819 12.378 1.00 25.45 O -ATOM 474 ND2 ASN A 60 16.924 20.586 11.216 1.00 24.09 N -ATOM 475 N ILE A 61 20.717 22.964 12.260 1.00 11.08 N -ATOM 476 CA ILE A 61 21.184 24.263 11.690 1.00 11.78 C -ATOM 477 C ILE A 61 21.110 24.111 10.173 1.00 13.74 C -ATOM 478 O ILE A 61 21.841 23.198 9.686 1.00 14.60 O -ATOM 479 CB ILE A 61 22.650 24.516 12.172 1.00 11.80 C -ATOM 480 CG1 ILE A 61 22.662 24.819 13.699 1.00 11.56 C -ATOM 481 CG2 ILE A 61 23.376 25.645 11.409 1.00 13.29 C -ATOM 482 CD1 ILE A 61 24.123 24.981 14.195 1.00 11.42 C -ATOM 483 N GLN A 62 20.291 24.875 9.507 1.00 13.97 N -ATOM 484 CA GLN A 62 20.081 24.773 8.033 1.00 15.52 C -ATOM 485 C GLN A 62 20.822 25.914 7.332 1.00 13.94 C -ATOM 486 O GLN A 62 21.323 26.830 8.008 1.00 12.15 O -ATOM 487 CB GLN A 62 18.599 24.736 7.727 1.00 19.53 C -ATOM 488 CG GLN A 62 17.819 23.434 7.900 1.00 26.38 C -ATOM 489 CD GLN A 62 16.509 23.529 7.116 1.00 30.61 C -ATOM 490 OE1 GLN A 62 15.446 22.980 7.433 1.00 33.23 O -ATOM 491 NE2 GLN A 62 16.539 24.293 6.009 1.00 32.71 N -ATOM 492 N LYS A 63 20.924 25.862 6.006 1.00 11.73 N -ATOM 493 CA LYS A 63 21.656 26.847 5.240 1.00 11.97 C -ATOM 494 C LYS A 63 21.127 28.240 5.574 1.00 10.41 C -ATOM 495 O LYS A 63 19.958 28.465 5.842 1.00 9.59 O -ATOM 496 CB LYS A 63 21.631 26.642 3.731 1.00 13.73 C -ATOM 497 CG LYS A 63 20.210 26.423 3.175 1.00 16.98 C -ATOM 498 CD LYS A 63 20.268 26.589 1.656 1.00 20.19 C -ATOM 499 CE LYS A 63 19.202 25.857 0.891 1.00 23.42 C -ATOM 500 NZ LYS A 63 17.884 26.544 1.075 1.00 25.97 N -ATOM 501 N GLU A 64 22.099 29.163 5.605 1.00 10.04 N -ATOM 502 CA GLU A 64 21.907 30.563 5.881 1.00 10.94 C -ATOM 503 C GLU A 64 21.466 30.953 7.261 1.00 9.74 C -ATOM 504 O GLU A 64 21.066 32.112 7.533 1.00 9.42 O -ATOM 505 CB GLU A 64 21.023 31.223 4.784 1.00 18.31 C -ATOM 506 CG GLU A 64 21.861 31.342 3.474 1.00 24.16 C -ATOM 507 CD GLU A 64 21.156 30.726 2.311 1.00 29.00 C -ATOM 508 OE1 GLU A 64 19.942 30.793 2.170 1.00 31.72 O -ATOM 509 OE2 GLU A 64 21.954 30.152 1.535 1.00 32.61 O -ATOM 510 N SER A 65 21.674 30.034 8.191 1.00 6.85 N -ATOM 511 CA SER A 65 21.419 30.253 9.620 1.00 6.90 C -ATOM 512 C SER A 65 22.504 31.228 10.136 1.00 4.72 C -ATOM 513 O SER A 65 23.579 31.321 9.554 1.00 3.91 O -ATOM 514 CB SER A 65 21.637 28.923 10.353 1.00 7.28 C -ATOM 515 OG SER A 65 20.544 28.047 10.059 1.00 10.56 O -ATOM 516 N THR A 66 22.241 31.873 11.241 1.00 4.48 N -ATOM 517 CA THR A 66 23.212 32.762 11.891 1.00 3.80 C -ATOM 518 C THR A 66 23.509 32.224 13.290 1.00 4.60 C -ATOM 519 O THR A 66 22.544 31.942 14.034 1.00 5.33 O -ATOM 520 CB THR A 66 22.699 34.267 11.985 1.00 2.85 C -ATOM 521 OG1 THR A 66 22.495 34.690 10.589 1.00 2.15 O -ATOM 522 CG2 THR A 66 23.727 35.131 12.722 1.00 3.40 C -ATOM 523 N LEU A 67 24.790 32.021 13.618 1.00 4.17 N -ATOM 524 CA LEU A 67 25.149 31.609 14.980 1.00 3.85 C -ATOM 525 C LEU A 67 25.698 32.876 15.669 1.00 3.80 C -ATOM 526 O LEU A 67 26.158 33.730 14.894 1.00 5.54 O -ATOM 527 CB LEU A 67 26.310 30.594 14.967 1.00 7.18 C -ATOM 528 CG LEU A 67 26.290 29.480 13.960 1.00 9.67 C -ATOM 529 CD1 LEU A 67 27.393 28.442 14.229 1.00 8.12 C -ATOM 530 CD2 LEU A 67 24.942 28.807 13.952 1.00 11.66 C -ATOM 531 N HIS A 68 25.621 32.945 16.950 1.00 2.94 N -ATOM 532 CA HIS A 68 26.179 34.127 17.650 1.00 4.17 C -ATOM 533 C HIS A 68 27.475 33.651 18.304 1.00 5.32 C -ATOM 534 O HIS A 68 27.507 32.587 18.958 1.00 7.70 O -ATOM 535 CB HIS A 68 25.214 34.565 18.780 1.00 5.57 C -ATOM 536 CG HIS A 68 23.978 35.121 18.126 1.00 9.95 C -ATOM 537 ND1 HIS A 68 23.853 36.432 17.781 1.00 13.74 N -ATOM 538 CD2 HIS A 68 22.824 34.514 17.782 1.00 12.79 C -ATOM 539 CE1 HIS A 68 22.674 36.627 17.200 1.00 14.75 C -ATOM 540 NE2 HIS A 68 22.045 35.455 17.173 1.00 16.30 N -ATOM 541 N LEU A 69 28.525 34.447 18.189 1.00 5.29 N -ATOM 542 CA LEU A 69 29.801 34.145 18.829 1.00 3.97 C -ATOM 543 C LEU A 69 30.052 35.042 20.004 1.00 5.07 C -ATOM 544 O LEU A 69 30.105 36.305 19.788 1.00 4.34 O -ATOM 545 CB LEU A 69 30.925 34.304 17.753 1.00 6.08 C -ATOM 546 CG LEU A 69 32.345 34.183 18.358 1.00 7.37 C -ATOM 547 CD1 LEU A 69 32.555 32.783 18.870 1.00 6.87 C -ATOM 548 CD2 LEU A 69 33.361 34.491 17.245 1.00 9.96 C -ATOM 549 N VAL A 70 30.124 34.533 21.191 1.00 4.29 N -ATOM 550 CA VAL A 70 30.479 35.369 22.374 1.00 6.26 C -ATOM 551 C VAL A 70 31.901 34.910 22.728 1.00 9.22 C -ATOM 552 O VAL A 70 32.190 33.696 22.635 1.00 9.36 O -ATOM 553 CB VAL A 70 29.472 35.181 23.498 1.00 8.69 C -ATOM 554 CG1 VAL A 70 29.821 35.957 24.765 1.00 9.76 C -ATOM 555 CG2 VAL A 70 28.049 35.454 23.071 1.00 8.54 C -ATOM 556 N LEU A 71 32.763 35.831 23.090 1.00 12.71 N -ATOM 557 CA LEU A 71 34.145 35.472 23.481 1.00 16.06 C -ATOM 558 C LEU A 71 34.239 35.353 24.979 1.00 18.09 C -ATOM 559 O LEU A 71 33.707 36.197 25.728 1.00 19.26 O -ATOM 560 CB LEU A 71 35.114 36.564 22.907 1.00 17.10 C -ATOM 561 CG LEU A 71 35.926 35.979 21.737 1.00 19.37 C -ATOM 562 CD1 LEU A 71 35.003 35.084 20.920 1.00 17.51 C -ATOM 563 CD2 LEU A 71 36.533 37.087 20.917 1.00 19.57 C -ATOM 564 N ARG A 72 34.930 34.384 25.451 1.00 21.47 N -ATOM 565 CA ARG A 72 35.161 34.174 26.896 1.00 25.83 C -ATOM 566 C ARG A 72 36.671 34.296 27.089 1.00 27.74 C -ATOM 567 O ARG A 72 37.305 33.233 26.795 1.00 30.65 O -ATOM 568 CB ARG A 72 34.717 32.760 27.286 1.00 28.49 C -ATOM 569 CG ARG A 72 35.752 32.054 28.160 1.00 31.79 C -ATOM 570 CD ARG A 72 35.612 30.577 28.044 1.00 34.05 C -ATOM 571 NE ARG A 72 35.040 30.252 26.730 1.00 35.08 N -ATOM 572 CZ ARG A 72 34.338 29.103 26.650 1.00 34.67 C -ATOM 573 NH1 ARG A 72 34.110 28.437 27.768 1.00 35.02 N -ATOM 574 NH2 ARG A 72 34.014 28.657 25.457 1.00 34.97 N -ATOM 575 N LEU A 73 37.197 35.397 27.513 0.45 28.93 N -ATOM 576 CA LEU A 73 38.668 35.502 27.680 0.45 30.76 C -ATOM 577 C LEU A 73 39.076 34.931 29.031 0.45 32.18 C -ATOM 578 O LEU A 73 38.297 34.946 29.996 0.45 32.31 O -ATOM 579 CB LEU A 73 39.080 36.941 27.406 0.45 30.53 C -ATOM 580 CG LEU A 73 39.502 37.340 26.002 0.45 30.16 C -ATOM 581 CD1 LEU A 73 38.684 36.647 24.923 0.45 29.57 C -ATOM 582 CD2 LEU A 73 39.337 38.854 25.862 0.45 29.11 C -ATOM 583 N ARG A 74 40.294 34.412 29.045 0.45 33.82 N -ATOM 584 CA ARG A 74 40.873 33.802 30.253 0.45 35.33 C -ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C -ATOM 586 O ARG A 74 42.945 34.994 30.583 0.45 36.70 O -ATOM 587 CB ARG A 74 41.651 32.529 29.923 0.45 36.91 C -ATOM 588 CG ARG A 74 41.608 31.444 30.989 0.45 38.62 C -ATOM 589 CD ARG A 74 41.896 30.080 30.456 0.45 39.75 C -ATOM 590 NE ARG A 74 43.311 29.735 30.563 0.45 41.13 N -ATOM 591 CZ ARG A 74 44.174 29.905 29.554 0.45 41.91 C -ATOM 592 NH1 ARG A 74 43.754 30.312 28.356 0.45 42.75 N -ATOM 593 NH2 ARG A 74 45.477 29.726 29.763 0.45 41.93 N -ATOM 594 N GLY A 75 41.165 35.531 31.898 0.25 36.31 N -ATOM 595 CA GLY A 75 41.845 36.550 32.686 0.25 36.07 C -ATOM 596 C GLY A 75 41.251 37.941 32.588 0.25 36.16 C -ATOM 597 O GLY A 75 41.102 38.523 31.500 0.25 36.26 O -ATOM 598 N GLY A 76 40.946 38.472 33.757 0.25 36.05 N -ATOM 599 CA GLY A 76 40.373 39.813 33.944 0.25 36.19 C -ATOM 600 C GLY A 76 40.031 39.992 35.432 0.25 36.20 C -ATOM 601 O GLY A 76 38.933 40.525 35.687 0.25 36.13 O -ATOM 602 OXT GLY A 76 40.862 39.575 36.251 0.25 36.27 O -TER 603 GLY A 76 -HETATM 604 O HOH A 77 45.747 30.081 19.708 1.00 12.43 O -HETATM 605 O HOH A 78 19.168 31.868 17.050 1.00 12.65 O -HETATM 606 O HOH A 79 32.010 38.387 19.636 1.00 12.83 O -HETATM 607 O HOH A 80 42.084 27.361 21.953 1.00 22.27 O -HETATM 608 O HOH A 81 21.314 20.644 8.719 1.00 18.33 O -HETATM 609 O HOH A 82 31.965 38.637 3.699 1.00 31.69 O -HETATM 610 O HOH A 83 27.707 15.908 4.653 1.00 20.30 O -HETATM 611 O HOH A 84 19.969 32.720 14.769 1.00 10.14 O -HETATM 612 O HOH A 85 29.847 13.577 10.864 1.00 29.65 O -HETATM 613 O HOH A 86 23.893 27.864 1.501 1.00 23.48 O -HETATM 614 O HOH A 87 19.638 23.312 4.775 1.00 18.40 O -HETATM 615 O HOH A 88 34.628 29.369 4.779 1.00 26.17 O -HETATM 616 O HOH A 89 42.240 24.744 25.707 1.00 31.34 O -HETATM 617 O HOH A 90 30.290 42.500 8.820 1.00 16.49 O -HETATM 618 O HOH A 91 24.512 39.162 10.841 1.00 13.14 O -HETATM 619 O HOH A 92 26.557 43.450 19.940 1.00 19.38 O -HETATM 620 O HOH A 93 42.535 22.385 13.872 1.00 29.35 O -HETATM 621 O HOH A 94 42.440 26.381 12.686 1.00 29.46 O -HETATM 622 O HOH A 95 22.651 14.457 13.085 1.00 22.07 O -HETATM 623 O HOH A 96 35.325 26.551 23.202 1.00 15.20 O -HETATM 624 O HOH A 97 23.629 20.940 3.146 1.00 15.45 O -HETATM 625 O HOH A 98 25.928 21.774 2.325 1.00 13.70 O -HETATM 626 O HOH A 99 33.388 21.973 5.659 1.00 24.89 O -HETATM 627 O HOH A 100 18.326 23.911 17.697 1.00 24.10 O -HETATM 628 O HOH A 101 18.160 27.072 10.662 1.00 20.76 O -HETATM 629 O HOH A 102 34.746 17.167 18.219 1.00 32.86 O -HETATM 630 O HOH A 103 19.801 32.364 20.210 1.00 21.09 O -HETATM 631 O HOH A 104 30.285 26.829 22.191 1.00 8.56 O -HETATM 632 O HOH A 105 44.612 32.306 16.961 1.00 7.69 O -HETATM 633 O HOH A 106 16.287 25.999 13.142 0.78 28.90 O -HETATM 634 O HOH A 107 27.101 42.135 15.494 0.51 23.36 O -HETATM 635 O HOH A 108 37.209 23.795 21.367 0.74 27.88 O -HETATM 636 O HOH A 109 19.582 32.034 -0.685 0.49 22.24 O -HETATM 637 O HOH A 110 28.824 25.094 0.886 0.77 36.99 O -HETATM 638 O HOH A 111 25.146 19.162 25.323 0.87 36.70 O -HETATM 639 O HOH A 112 20.747 37.769 14.674 0.85 29.64 O -HETATM 640 O HOH A 113 16.035 17.841 8.765 0.61 23.89 O -HETATM 641 O HOH A 114 35.712 46.814 12.926 0.48 27.11 O -HETATM 642 O HOH A 115 15.570 27.475 7.482 0.51 24.18 O -HETATM 643 O HOH A 116 33.447 21.075 2.918 0.59 26.03 O -HETATM 644 O HOH A 117 41.116 39.021 13.061 0.63 22.39 O -HETATM 645 O HOH A 118 32.346 13.689 18.912 0.48 24.09 O -HETATM 646 O HOH A 119 31.197 13.048 7.920 0.71 29.54 O -HETATM 647 O HOH A 120 42.853 39.375 29.308 0.64 46.90 O -HETATM 648 O HOH A 121 39.646 23.959 9.699 0.41 18.25 O -HETATM 649 O HOH A 122 34.405 45.181 13.420 0.87 26.13 O -HETATM 650 O HOH A 123 26.517 24.300 27.592 0.41 21.02 O -HETATM 651 O HOH A 124 40.740 38.734 9.602 0.45 16.60 O -HETATM 652 O HOH A 125 31.494 18.276 23.170 0.67 26.53 O -HETATM 653 O HOH A 126 37.752 30.947 1.059 0.87 32.52 O -HETATM 654 O HOH A 127 31.771 16.941 7.511 0.64 15.94 O -HETATM 655 O HOH A 128 41.628 24.537 10.145 0.57 22.53 O -HETATM 656 O HOH A 129 28.988 22.175 -1.744 0.56 29.32 O -HETATM 657 O HOH A 130 14.882 16.539 10.692 0.53 24.82 O -HETATM 658 O HOH A 131 32.589 40.385 7.523 0.36 26.01 O -HETATM 659 O HOH A 132 38.363 30.369 5.579 0.49 35.45 O -HETATM 660 O HOH A 133 27.841 46.062 17.589 0.81 32.15 O -HETATM 661 O HOH A 134 37.667 43.421 17.000 0.50 33.32 O -MASTER 275 0 0 2 5 9 0 6 660 1 0 6 -END diff --git a/example/1ubq.ss b/example/1ubq.ss deleted file mode 100644 index 030dab3..0000000 --- a/example/1ubq.ss +++ /dev/null @@ -1 +0,0 @@ -cbbbbbcccccbbbbbccccccaaaaaaaaaaaacccaaabbbbbccbbccccccaaaaccccc diff --git a/example/bmr18583_3.str b/example/bmr18583_3.str new file mode 100644 index 0000000..a2acf18 --- /dev/null +++ b/example/bmr18583_3.str @@ -0,0 +1,1945 @@ +data_18583 + +####################### +# Entry information # +####################### + +save_entry_information + _Entry.Sf_category entry_information + _Entry.Sf_framecode entry_information + _Entry.ID 18583 + _Entry.Title +; +Solution structure of the gp78CUE/K48-Ub2 complex +; + _Entry.Type macromolecule + _Entry.Version_type original + _Entry.Submission_date 2012-07-09 + _Entry.Accession_date 2012-07-09 + _Entry.Last_release_date . + _Entry.Original_release_date . + _Entry.Origination author + _Entry.NMR_STAR_version 3.1.1.61 + _Entry.Original_NMR_STAR_version 3.1 + _Entry.Experimental_method NMR + _Entry.Experimental_method_subtype SOLUTION + _Entry.Details 'Amide shifts of gp78CUE and distal Ubiquitin in the gp78CUE/K48-Ub2 complex' + _Entry.BMRB_internal_directory_name . + + loop_ + _Entry_author.Ordinal + _Entry_author.Given_name + _Entry_author.Family_name + _Entry_author.First_initial + _Entry_author.Middle_initials + _Entry_author.Family_title + _Entry_author.Entry_ID + + 1 Shan Liu . . . 18583 + 2 Yinghua Chen . . . 18583 + 3 Tao Huang . . . 18583 + 4 Sergey Tarasov . G. . 18583 + 5 Aaren King . . . 18583 + 6 Jess Li . . . 18583 + 7 Allan Weissman . M. . 18583 + 8 Robert Byrd . A. . 18583 + 9 Ranabir Das . . . 18583 + + stop_ + + loop_ + _SG_project.SG_project_ID + _SG_project.Project_name + _SG_project.Full_name_of_center + _SG_project.Initial_of_center + _SG_project.Entry_ID + + 1 'not applicable' 'not applicable' . 18583 + + stop_ + + loop_ + _Struct_keywords.Keywords + _Struct_keywords.Text + _Struct_keywords.Entry_ID + + CUE . 18583 + gp78 . 18583 + NMR . 18583 + Protein . 18583 + + stop_ + + loop_ + _Data_set.Type + _Data_set.Count + _Data_set.Entry_ID + + assigned_chemical_shifts 1 18583 + + stop_ + + loop_ + _Datum.Type + _Datum.Count + _Datum.Entry_ID + + '15N chemical shifts' 111 18583 + '1H chemical shifts' 111 18583 + + stop_ + + loop_ + _Release.Release_number + _Release.Format_type + _Release.Format_version + _Release.Date + _Release.Submission_date + _Release.Type + _Release.Author + _Release.Detail + _Release.Entry_ID + + 2 . . 2013-02-19 2012-07-09 update BMRB 'update entry citation' 18583 + 1 . . 2012-11-19 2012-07-09 original author 'original release' 18583 + + stop_ + + loop_ + _Related_entries.Database_name + _Related_entries.Database_accession_code + _Related_entries.Relationship + _Related_entries.Entry_ID + + BMRB 18581 'gp78 CUE domain' 18583 + BMRB 18582 'gp78CUE bound to ubiquitin' 18583 + BMRB 18584 'gp78CUE/K48-Ub2 complex' 18583 + PDB 2LVP 'BMRB Entry Tracking System' 18583 + + stop_ + +save_ + + +############### +# Citations # +############### + +save_entry_citation + _Citation.Sf_category citations + _Citation.Sf_framecode entry_citation + _Citation.Entry_ID 18583 + _Citation.ID 1 + _Citation.Class 'entry citation' + _Citation.CAS_abstract_code . + _Citation.MEDLINE_UI_code . + _Citation.DOI . + _Citation.PubMed_ID 23123110 + _Citation.Full_citation . + _Citation.Title 'Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains.' + _Citation.Status published + _Citation.Type journal + _Citation.Journal_abbrev Structure + _Citation.Journal_name_full 'Structure (London, England : 1993)' + _Citation.Journal_volume 20 + _Citation.Journal_issue 12 + _Citation.Journal_ASTM . + _Citation.Journal_ISSN . + _Citation.Journal_CSD . + _Citation.Book_title . + _Citation.Book_chapter_title . + _Citation.Book_volume . + _Citation.Book_series . + _Citation.Book_publisher . + _Citation.Book_publisher_city . + _Citation.Book_ISBN . + _Citation.Conference_title . + _Citation.Conference_site . + _Citation.Conference_state_province . + _Citation.Conference_country . + _Citation.Conference_start_date . + _Citation.Conference_end_date . + _Citation.Conference_abstract_number . + _Citation.Thesis_institution . + _Citation.Thesis_institution_city . + _Citation.Thesis_institution_country . + _Citation.WWW_URL . + _Citation.Page_first 2138 + _Citation.Page_last 2150 + _Citation.Year 2012 + _Citation.Details . + + loop_ + _Citation_author.Ordinal + _Citation_author.Given_name + _Citation_author.Family_name + _Citation_author.First_initial + _Citation_author.Middle_initials + _Citation_author.Family_title + _Citation_author.Entry_ID + _Citation_author.Citation_ID + + 1 Shan Liu . . . 18583 1 + 2 Yinghua Chen . . . 18583 1 + 3 Jess Li . . . 18583 1 + 4 Tao Huang . . . 18583 1 + 5 Sergey Tarasov . . . 18583 1 + 6 Aaren King . . . 18583 1 + 7 Allan Weissman . M. . 18583 1 + 8 'R. Andrew' Byrd . . . 18583 1 + 9 Ranabir Das . . . 18583 1 + + stop_ + +save_ + + +############################################# +# Molecular system (assembly) description # +############################################# + +save_assembly + _Assembly.Sf_category assembly + _Assembly.Sf_framecode assembly + _Assembly.Entry_ID 18583 + _Assembly.ID 1 + _Assembly.Name 'gp78CUE/K48-Ub2 complex' + _Assembly.BMRB_code . + _Assembly.Number_of_components 3 + _Assembly.Organic_ligands . + _Assembly.Metal_ions . + _Assembly.Non_standard_bonds . + _Assembly.Ambiguous_conformational_states . + _Assembly.Ambiguous_chem_comp_sites . + _Assembly.Molecules_in_chemical_exchange . + _Assembly.Paramagnetic no + _Assembly.Thiol_state . + _Assembly.Molecular_mass . + _Assembly.Enzyme_commission_number . + _Assembly.Details . + _Assembly.DB_query_date . + _Assembly.DB_query_revised_last_date . + + loop_ + _Entity_assembly.ID + _Entity_assembly.Entity_assembly_name + _Entity_assembly.Entity_ID + _Entity_assembly.Entity_label + _Entity_assembly.Asym_ID + _Entity_assembly.PDB_chain_ID + _Entity_assembly.Experimental_data_reported + _Entity_assembly.Physical_state + _Entity_assembly.Conformational_isomer + _Entity_assembly.Chemical_exchange_state + _Entity_assembly.Magnetic_equivalence_group_code + _Entity_assembly.Role + _Entity_assembly.Details + _Entity_assembly.Entry_ID + _Entity_assembly.Assembly_ID + + 1 ubiquitin_1 1 $entity_1 A . yes native no no . . . 18583 1 + 2 gp78CUE 2 $entity_2 C . yes native no no . . . 18583 1 + + stop_ + +save_ + + + #################################### + # Biological polymers and ligands # + #################################### + +save_entity_1 + _Entity.Sf_category entity + _Entity.Sf_framecode entity_1 + _Entity.Entry_ID 18583 + _Entity.ID 1 + _Entity.BMRB_code . + _Entity.Name ubiquitin + _Entity.Type polymer + _Entity.Polymer_common_type . + _Entity.Polymer_type polypeptide(L) + _Entity.Polymer_type_details . + _Entity.Polymer_strand_ID A,B + _Entity.Polymer_seq_one_letter_code_can . + _Entity.Polymer_seq_one_letter_code +; +MQIFVKTLTGKTITLEVEPS +DTIENVKAKIQDKEGIPPDQ +QRLIFAGKQLEDGRTLSDYN +IQKESTLHLVLRLRGG +; + _Entity.Target_identifier . + _Entity.Polymer_author_defined_seq . + _Entity.Polymer_author_seq_details . + _Entity.Ambiguous_conformational_states no + _Entity.Ambiguous_chem_comp_sites no + _Entity.Nstd_monomer no + _Entity.Nstd_chirality no + _Entity.Nstd_linkage no + _Entity.Nonpolymer_comp_ID . + _Entity.Nonpolymer_comp_label . + _Entity.Number_of_monomers 76 + _Entity.Number_of_nonpolymer_components . + _Entity.Paramagnetic no + _Entity.Thiol_state 'not present' + _Entity.Src_method man + _Entity.Parent_entity_ID . + _Entity.Fragment . + _Entity.Mutation . + _Entity.EC_number . + _Entity.Calc_isoelectric_point . + _Entity.Formula_weight 8576.914 + _Entity.Formula_weight_exptl . + _Entity.Formula_weight_exptl_meth . + _Entity.Details . + _Entity.DB_query_date . + _Entity.DB_query_revised_last_date 2015-11-25 + + loop_ + _Entity_db_link.Ordinal + _Entity_db_link.Author_supplied + _Entity_db_link.Database_code + _Entity_db_link.Accession_code + _Entity_db_link.Entry_mol_code + _Entity_db_link.Entry_mol_name + _Entity_db_link.Entry_experimental_method + _Entity_db_link.Entry_structure_resolution + _Entity_db_link.Entry_relation_type + _Entity_db_link.Entry_details + _Entity_db_link.Chimera_segment_ID + _Entity_db_link.Seq_query_to_submitted_percent + _Entity_db_link.Seq_subject_length + _Entity_db_link.Seq_identity + _Entity_db_link.Seq_positive + _Entity_db_link.Seq_homology_expectation_val + _Entity_db_link.Seq_align_begin + _Entity_db_link.Seq_align_end + _Entity_db_link.Seq_difference_details + _Entity_db_link.Seq_alignment_details + _Entity_db_link.Entry_ID + _Entity_db_link.Entity_ID + + 1 no BMRB 11505 . entity . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 2 no BMRB 11547 . ubiquitin . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 3 no BMRB 15047 . denatured_ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 4 no BMRB 15410 . Ubi . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 5 no BMRB 15689 . UBB . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 6 no BMRB 15907 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 7 no BMRB 16228 . ubiquitin . . . . . 100.00 76 97.37 98.68 1.73e-44 . . . . 18583 1 + 8 no BMRB 16582 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 9 no BMRB 16626 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 10 no BMRB 16895 . UBB+1 . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 11 no BMRB 17181 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 12 no BMRB 17439 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 13 no BMRB 17769 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 14 no BMRB 17919 . entity . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 15 no BMRB 18582 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 16 no BMRB 18584 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 17 no BMRB 18610 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 18 no BMRB 18611 . Ubiquitin_A_state . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 19 no BMRB 18737 . UBIQUITIN . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 20 no BMRB 19406 . entity . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 21 no BMRB 19412 . entity . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 22 no BMRB 25070 . Ubiquitin . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 23 no BMRB 25123 . Ubiquitin . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 24 no BMRB 25601 . entity_1 . . . . . 100.00 76 97.37 97.37 5.31e-44 . . . . 18583 1 + 25 no BMRB 26604 . Ubiquitin_(microcrystalline) . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 26 no BMRB 4245 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 27 no BMRB 4375 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 28 no PDB 1AAR . "Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 29 no PDB 1CMX . "Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 30 no PDB 1D3Z . "Ubiquitin Nmr Structure" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 31 no PDB 1F9J . "Structure Of A New Crystal Form Of Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 32 no PDB 1FXT . "Structure Of A Conjugating Enzyme-Ubiquitin Thiolester Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 33 no PDB 1G6J . "Structure Of Recombinant Human Ubiquitin In Aot Reverse Micelles" . . . . . 98.68 76 100.00 100.00 7.58e-45 . . . . 18583 1 + 34 no PDB 1GJZ . "Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin" . . . . . 67.11 53 100.00 100.00 3.14e-26 . . . . 18583 1 + 35 no PDB 1NBF . "Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme In Isolation And In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 36 no PDB 1OGW . "Synthetic Ubiquitin With Fluoro-Leu At 50 And 67" . . . . . 100.00 76 97.37 97.37 2.65e-44 . . . . 18583 1 + 37 no PDB 1P3Q . "Mechanism Of Ubiquitin Recognition By The Cue Domain Of Vps9" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 38 no PDB 1Q5W . "Ubiquitin Recognition By Npl4 Zinc-Fingers" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 39 no PDB 1S1Q . "Tsg101(Uev) Domain In Complex With Ubiquitin" . . . . . 98.68 76 100.00 100.00 7.58e-45 . . . . 18583 1 + 40 no PDB 1TBE . "Structure Of Tetraubiquitin Shows How Multiubiquitin Chains Can Be Formed" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 41 no PDB 1UBI . "Synthetic Structural And Biological Studies Of The Ubiquitin System. Part 1" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 42 no PDB 1UBQ . "Structure Of Ubiquitin Refined At 1.8 Angstroms Resolution" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 43 no PDB 1UZX . "A Complex Of The Vps23 Uev With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 44 no PDB 1V80 . "Solution Structures Of Ubiquitin At 30 Bar And 3 Kbar" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 45 no PDB 1V81 . "Solution Structures Of Ubiquitin At 30 Bar And 3 Kbar" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 46 no PDB 1VX7 . "Cryo-em Structure Of The Plasmodium Falciparum 80s Ribosome Bound To The Anti-protozoan Drug Emetine, Large Subunit (protein On" . . . . . 100.00 128 98.68 100.00 1.38e-45 . . . . 18583 1 + 47 no PDB 1WR6 . "Crystal Structure Of Gga3 Gat Domain In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 48 no PDB 1WRD . "Crystal Structure Of Tom1 Gat Domain In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 49 no PDB 1XD3 . "Crystal Structure Of Uchl3-Ubvme Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 50 no PDB 1XQQ . "Simultaneous Determination Of Protein Structure And Dynamics" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 51 no PDB 1YD8 . "Complex Of Human Gga3 Gat Domain And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 52 no PDB 1YIW . "X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin" . . . . . 100.00 76 98.68 100.00 2.84e-45 . . . . 18583 1 + 53 no PDB 1YJ1 . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 54 no PDB 1YX5 . "Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX" . . . . . 100.00 98 100.00 100.00 2.31e-46 . . . . 18583 1 + 55 no PDB 1YX6 . "Solution Structure Of S5a Uim-2UBIQUITIN COMPLEX" . . . . . 100.00 98 100.00 100.00 2.31e-46 . . . . 18583 1 + 56 no PDB 1ZGU . "Solution Structure Of The Human Mms2-Ubiquitin Complex" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 57 no PDB 2AYO . "Structure Of Usp14 Bound To Ubquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 58 no PDB 2BGF . "Nmr Structure Of Lys48-Linked Di-Ubiquitin Using Chemical Shift Perturbation Data Together With Rdcs And 15n- Relaxation Data" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 59 no PDB 2C7M . "Human Rabex-5 Residues 1-74 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 60 no PDB 2C7N . "Human Rabex-5 Residues 1-74 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 61 no PDB 2D3G . "Double Sided Ubiquitin Binding Of Hrs-Uim" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 62 no PDB 2DEN . "Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 63 no PDB 2DX5 . "The Complex Structure Between The Mouse Eap45-Glue Domain And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 64 no PDB 2FCM . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 65 no PDB 2FCN . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Val35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 66 no PDB 2FCQ . "X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin With A Cubic Space Group" . . . . . 100.00 76 98.68 100.00 2.84e-45 . . . . 18583 1 + 67 no PDB 2FCS . "X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.83e-44 . . . . 18583 1 + 68 no PDB 2FID . "Crystal Structure Of A Bovine Rabex-5 Fragment Complexed With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 69 no PDB 2FIF . "Crystal Structure Of A Bovine Rabex-5 Fragment Complexed With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 70 no PDB 2FUH . "Solution Structure Of The Ubch5cUB NON-Covalent Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 71 no PDB 2G45 . "Co-Crystal Structure Of Znf Ubp Domain From The Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 72 no PDB 2GMI . Mms2UBC13~UBIQUITIN . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 73 no PDB 2HD5 . "Usp2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 74 no PDB 2HTH . "Structural Basis For Ubiquitin Recognition By The Human Eap45ESCRT-Ii Glue Domain" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 75 no PDB 2IBI . "Covalent Ubiquitin-Usp2 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 76 no PDB 2J7Q . "Crystal Structure Of The Ubiquitin-Specific Protease Encoded By Murine Cytomegalovirus Tegument Protein M48 In Complex With A U" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 77 no PDB 2JF5 . "Crystal Structure Of Lys63-Linked Di-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 78 no PDB 2JRI . "Solution Structure Of The Josephin Domain Of Ataxin-3 In Complex With Ubiquitin Molecule." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 79 no PDB 2JY6 . "Solution Structure Of The Complex Of Ubiquitin And Ubiquilin 1 Uba Domain" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 80 no PDB 2JZZ . "Solid-State Nmr Structure Of Microcrystalline Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 81 no PDB 2K25 . "Automated Nmr Structure Of The Ubb By Fapsy" . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 82 no PDB 2K39 . "Recognition Dynamics Up To Microseconds Revealed From Rdc Derived Ubiquitin Ensemble In Solution" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 83 no PDB 2K6D . "Cin85 Sh3-C Domain In Complex With Ubiquitin" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 84 no PDB 2K8B . "Solution Structure Of Plaa Family Ubiquitin Binding Domain (Pfuc) Cis Isomer In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 85 no PDB 2K8C . "Solution Structure Of Plaa Family Ubiquitin Binding Domain (Pfuc) Trans Isomer In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 86 no PDB 2KDE . "Nmr Structure Of Major S5a (196-306):k48 Linked Diubiquitin Species" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 87 no PDB 2KDF . "Nmr Structure Of Minor S5a (196-306):k48 Linked Diubiquitin Species" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 88 no PDB 2KHW . "Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 89 no PDB 2KJH . "Nmr Based Structural Model Of The Ubch8-Ubiquitin Complex" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 90 no PDB 2KLG . "Pere Nmr Structure Of Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 91 no PDB 2KN5 . "A Correspondence Between Solution-State Dynamics Of An Individual Protein And The Sequence And Conformational Diversity Of Its " . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 92 no PDB 2KOX . "Nmr Residual Dipolar Couplings Identify Long Range Correlated Motions In The Backbone Of The Protein Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 93 no PDB 2KTF . "Solution Nmr Structure Of Human Polymerase Iota Ubm2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 94 no PDB 2KWU . "Solution Structure Of Ubm2 Of Murine Polymerase Iota In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 95 no PDB 2KWV . "Solution Structure Of Ubm1 Of Murine Polymerase Iota In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 96 no PDB 2KX0 . "The Solution Structure Of Ubb+1, Frameshift Mutant Of Ubiquitin B" . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 97 no PDB 2L0F . "Solution Nmr Structure Of Human Polymerase Iota Ubm2 (P692a Mutant) In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 98 no PDB 2L0T . "Solution Structure Of The Complex Of Ubiquitin And The Vhs Domain Of Stam2" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 99 no PDB 2L3Z . "Proton-Detected 4d Dream Solid-State Nmr Structure Of Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 100 no PDB 2LD9 . "Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs" . . . . . 100.00 77 100.00 100.00 7.92e-46 . . . . 18583 1 + 101 no PDB 2LJ5 . "Description Of The Structural Fluctuations Of Proteins From Structure- Based Calculations Of Residual Dipolar Couplings" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 102 no PDB 2LVO . "Structure Of The Gp78cue Domain Bound To Monubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 103 no PDB 2LVP . "Gp78cue Domain Bound To The Distal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 104 no PDB 2LVQ . "Gp78cue Domain Bound To The Proximal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 105 no PDB 2LZ6 . "Distinct Ubiquitin Binding Modes Exhibited By Sh3 Domains: Molecular Determinants And Functional Implications" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 106 no PDB 2MBB . "Solution Structure Of The Human Polymerase Iota Ubm1-ubiquitin Complex" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 107 no PDB 2MBH . "Nmr Structure Of Eklf(22-40)/ubiquitin Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 108 no PDB 2MBO . "K11-linked Diubiquitin Average Solution Structure At Ph 6.8, 0 Mm Nacl" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 109 no PDB 2MBQ . "K11-linked Diubiquitin Average Solution Structure At Ph 6.8, 150 Mm Nacl" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 110 no PDB 2MCN . "Distinct Ubiquitin Binding Modes Exhibited By Sh3 Domains: Molecular Determinants And Functional Implications" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 111 no PDB 2MJ5 . "Structure Of The Uba Domain Of Human Nbr1 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 112 no PDB 2MJB . "Solution Nmr Structure Of Ubiquitin Refined Against Dipolar Couplings In 4 Media" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 113 no PDB 2MOR . "A Tensor-free Method For The Structural And Dynamical Refinement Of Proteins Using Residual Dipolar Couplings" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 114 no PDB 2MRE . "Nmr Structure Of The Rad18-ubz/ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 115 no PDB 2MRO . "Structure Of The Complex Of Ubiquitin And The Uba Domain From Dna- Damage-inducible 1 Protein (ddi1)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 116 no PDB 2MSG . "Solid-state Nmr Structure Of Ubiquitin" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 117 no PDB 2MUR . "Solution Structure Of The Human Faap20 Ubz-ubiquitin Complex" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 118 no PDB 2MWS . "Structure Of The Complex Of Ubiquitin And The Ubiquitin-like (ubl) Domain Of Ddi1" . . . . . 100.00 76 98.68 98.68 4.40e-45 . . . . 18583 1 + 119 no PDB 2N2K . "Ensemble Structure Of The Closed State Of Lys63-linked Diubiquitin In The Absence Of A Ligand" . . . . . 93.42 71 100.00 100.00 6.21e-42 . . . . 18583 1 + 120 no PDB 2NR2 . "The Mumo (Minimal Under-Restraining Minimal Over- Restraining) Method For The Determination Of Native States Ensembles Of Prote" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 121 no PDB 2O6V . "Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 122 no PDB 2OJR . "Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag" . . . . . 100.00 111 100.00 100.00 2.29e-45 . . . . 18583 1 + 123 no PDB 2OOB . "Crystal Structure Of The Uba Domain From Cbl-B Ubiquitin Ligase In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 124 no PDB 2PE9 . "Nmr Based Structure Of The Open Conformation Of Lys48- Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tenso" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 125 no PDB 2PEA . "Nmr Based Structure Of The Closed Conformation Of Lys48- Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Ten" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 126 no PDB 2QHO . "Crystal Structure Of The Uba Domain From Edd Ubiquitin Ligase In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 127 no PDB 2RR9 . "The Solution Structure Of The K63-Ub2:tuims Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 128 no PDB 2RSU . "Alternative Structure Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 129 no PDB 2RU6 . "The Pure Alternative State Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 130 no PDB 2W9N . "Crystal Structure Of Linear Di-Ubiquitin" . . . . . 98.68 152 100.00 100.00 5.62e-44 . . . . 18583 1 + 131 no PDB 2WDT . "Crystal Structure Of Plasmodium Falciparum Uchl3 In Complex With The Suicide Inhibitor Ubvme" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 132 no PDB 2WWZ . "Tab2 Nzf Domain In Complex With Lys63-Linked Di-Ubiquitin, P212121" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 133 no PDB 2WX0 . "Tab2 Nzf Domain In Complex With Lys63-Linked Di-Ubiquitin, P21" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 134 no PDB 2WX1 . "Tab2 Nzf Domain In Complex With Lys63-Linked Tri-Ubiquitin, P212121" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 135 no PDB 2XBB . "Nedd4 Hect:ub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 136 no PDB 2XEW . "Crystal Structure Of K11-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 137 no PDB 2XK5 . "Crystal Structure Of K6-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 138 no PDB 2Y5B . "Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde" . . . . . 98.68 152 100.00 100.00 4.15e-44 . . . . 18583 1 + 139 no PDB 2Z59 . "Complex Structures Of Mouse Rpn13 (22-130aa) And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 140 no PDB 2ZCB . "Crystal Structure Of Ubiquitin P37aP38A" . . . . . 100.00 76 97.37 97.37 3.44e-44 . . . . 18583 1 + 141 no PDB 2ZCC . "Ubiquitin Crystallized Under High Pressure" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 142 no PDB 2ZNV . "Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 143 no PDB 2ZVN . "Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 144 no PDB 2ZVO . "Nemo Cozi Domain In Complex With Diubiquitin In C2 Space Group" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 145 no PDB 3A1Q . "Crystal Structure Of The Mouse Rap80 Uims In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 146 no PDB 3A33 . "Ubch5b~ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 147 no PDB 3A9J . "Crystal Structure Of The Mouse Tab2-Nzf In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 148 no PDB 3A9K . "Crystal Structure Of The Mouse Tab3-Nzf In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 149 no PDB 3AI5 . "Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein" . . . . . 97.37 307 100.00 100.00 1.64e-41 . . . . 18583 1 + 150 no PDB 3ALB . "Cyclic Lys48-Linked Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 151 no PDB 3AUL . "Crystal Structure Of Wild-Type Lys48-Linked Diubiquitin In An Open Conformation" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 152 no PDB 3AXC . "Crystal Structure Of Linear Diubiquitin" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 153 no PDB 3B08 . "Crystal Structure Of The Mouse Hoil1-l-nzf In Complex With Linear Di- Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 154 no PDB 3B0A . "Crystal Structure Of The Mouse Hoil1-l-nzf In Complex With Linear Di- Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 155 no PDB 3BY4 . "Structure Of Ovarian Tumor (Otu) Domain In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 156 no PDB 3C0R . "Structure Of Ovarian Tumor (Otu) Domain In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 157 no PDB 3DVG . "Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin" . . . . . 100.00 80 100.00 100.00 8.24e-46 . . . . 18583 1 + 158 no PDB 3DVN . "Crystal Structure Of K63-specific Fab Apu2.16 Bound To K63-linked Di- Ubiquitin" . . . . . 100.00 80 100.00 100.00 8.24e-46 . . . . 18583 1 + 159 no PDB 3EEC . "X-Ray Structure Of Human Ubiquitin Cd(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 160 no PDB 3EFU . "X-Ray Structure Of Human Ubiquitin-Hg(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 161 no PDB 3EHV . "X-Ray Structure Of Human Ubiquitin Zn(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 162 no PDB 3H1U . "Structure Of Ubiquitin In Complex With Cd Ions" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 163 no PDB 3H7P . "Crystal Structure Of K63-Linked Di-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 164 no PDB 3H7S . "Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture" . . . . . 100.00 76 98.68 98.68 2.81e-43 . . . . 18583 1 + 165 no PDB 3HM3 . "The Structure And Conformation Of Lys-63 Linked Tetra-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 166 no PDB 3I3T . "Crystal Structure Of Covalent Ubiquitin-usp21 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 167 no PDB 3IFW . "Crystal Structure Of The S18y Variant Of Ubiquitin Carboxy T Hydrolase L1 Bound To Ubiquitin Vinylmethylester." . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 168 no PDB 3IHP . "Covalent Ubiquitin-Usp5 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 169 no PDB 3JSV . "Crystal Structure Of Mouse Nemo Cozi In Complex With Lys63- Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 170 no PDB 3JVZ . E2~ubiquitin-Hect . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 171 no PDB 3JW0 . E2~ubiquitin-Hect . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 172 no PDB 3K9O . "The Crystal Structure Of E2-25k And Ubb+1 Complex" . . . . . 98.68 96 100.00 100.00 1.27e-44 . . . . 18583 1 + 173 no PDB 3K9P . "The Crystal Structure Of E2-25k And Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 174 no PDB 3KVF . "Crystal Structure Of The I93m Mutant Of Ubiquitin Carboxy Te Hydrolase L1 Bound To Ubiquitin Vinylmethylester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 175 no PDB 3KW5 . "Crystal Structure Of Ubiquitin Carboxy Terminal Hydrolase L1 Ubiquitin Vinylmethylester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 176 no PDB 3LDZ . "Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin" . . . . . 96.05 73 100.00 100.00 1.79e-43 . . . . 18583 1 + 177 no PDB 3M3J . "A New Crystal Form Of Lys48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 178 no PDB 3MHS . "Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 179 no PDB 3MTN . "Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor" . . . . . 88.16 85 98.51 98.51 1.47e-37 . . . . 18583 1 + 180 no PDB 3N30 . "Crystal Structure Of Cubic Zn3-Hub (Human Ubiquitin) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 181 no PDB 3N32 . "The Crystal Structure Of Human Ubiquitin Adduct With Zeise's Salt" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 182 no PDB 3NHE . "High Resolution Structure (1.26a) Of Usp2a In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 183 no PDB 3NOB . "Structure Of K11-linked Di-ubiquitin" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 184 no PDB 3NS8 . "Crystal Structure Of An Open Conformation Of Lys48-Linked Diubiquitin At Ph 7.5" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 185 no PDB 3O65 . "Crystal Structure Of A Josephin-Ubiquitin Complex: Evolutionary Restraints On Ataxin-3 Deubiquitinating Activity" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 186 no PDB 3OFI . "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 187 no PDB 3OJ3 . "Crystal Structure Of The A20 Znf4 And Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 188 no PDB 3OJ4 . "Crystal Structure Of The A20 Znf4, Ubiquitin And Ubch5a Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 189 no PDB 3ONS . "Crystal Structure Of Human Ubiquitin In A New Crystal Form" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 190 no PDB 3PHD . "Crystal Structure Of Human Hdac6 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 191 no PDB 3PHW . "Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 192 no PDB 3PRM . "Structural Analysis Of A Viral Otu Domain Protease From The Crimean- Congo Hemorrhagic Fever Virus In Complex With Human Ubiqui" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 193 no PDB 3PRP . "Structural Analysis Of A Viral Otu Domain Protease From The Crimean- Congo Hemorrhagic Fever Virus In Complex With Human Ubiqui" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 194 no PDB 3PT2 . "Structure Of A Viral Otu Domain Protease Bound To Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 195 no PDB 3PTF . "X-Ray Structure Of The Non-Covalent Complex Between Ubch5a And Ubiquitin" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 196 no PDB 3Q3F . "Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnas" . . . . . 98.68 189 100.00 100.00 5.35e-44 . . . . 18583 1 + 197 no PDB 3RUL . "New Strategy To Analyze Structures Of Glycopeptide-Target Complexes" . . . . . 98.68 79 100.00 100.00 3.97e-45 . . . . 18583 1 + 198 no PDB 3TBL . "Structure Of Mono-ubiquitinated Pcna: Implications For Dna Polymerase Switching And Okazaki Fragment Maturation" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 199 no PDB 3TMP . "The Catalytic Domain Of Human Deubiquitinase Duba In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 200 no PDB 3U30 . "Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin" . . . . . 100.00 172 100.00 100.00 6.89e-45 . . . . 18583 1 + 201 no PDB 3UGB . "Ubch5c~ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 202 no PDB 3VDZ . "Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms" . . . . . 100.00 111 100.00 100.00 1.47e-45 . . . . 18583 1 + 203 no PDB 3VFK . "The Structure Of Monodechloro-teicoplanin In Complex With Its Ligand, Using Ubiquitin As A Ligand Carrier" . . . . . 98.68 79 100.00 100.00 3.97e-45 . . . . 18583 1 + 204 no PDB 3VHT . "Crystal Structure Of Gfp-Wrnip1 Ubz Domain Fusion Protein In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 205 no PDB 3VUW . "Crystal Structure Of A20 Zf7 In Complex With Linear Ubiquitin, Form I" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 206 no PDB 3VUX . "Crystal Structure Of A20 Zf7 In Complex With Linear Ubiquitin, Form Ii" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 207 no PDB 3VUY . "Crystal Structure Of A20 Zf7 In Complex With Linear Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 208 no PDB 3WWQ . "Crystal Structure Of Faap20 Ubz Domain In Complex With Lys63-linked Diubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 209 no PDB 3WXE . "Crystal Structure Of Cyld Usp Domain (c596s) In Complex With Met1- Linked Diubiquitin" . . . . . 94.74 148 100.00 100.00 9.19e-42 . . . . 18583 1 + 210 no PDB 3WXF . "Crystal Structure Of Cyld Usp Domain (c596s E674q) In Complex With Met1-linked Diubiquitin" . . . . . 94.74 148 100.00 100.00 9.19e-42 . . . . 18583 1 + 211 no PDB 3WXG . "Crystal Structure Of Cyld Usp Domain (c596a) In Complex With Lys63- Linked Diubiquitin" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 212 no PDB 3ZLZ . "Lys6-linked Tri-ubiquitin" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 213 no PDB 3ZNH . "Crimean Congo Hemorrhagic Fever Virus Otu Domain In Complex With Ubiquitin-propargyl." . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 214 no PDB 3ZNI . "Structure Of Phosphotyr363-cbl-b - Ubch5b-ub - Zap-70 Peptide Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 215 no PDB 3ZNZ . "Crystal Structure Of Otulin Otu Domain (c129a) In Complex With Met1-di Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 216 no PDB 4A18 . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 217 no PDB 4A19 . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 2" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 218 no PDB 4A1B . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 3" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 219 no PDB 4A1D . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 4" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 220 no PDB 4ADX . "The Cryo-em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 221 no PDB 4AP4 . "Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 222 no PDB 4AUQ . "Structure Of Birc7-Ubch5b-Ub Complex." . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 223 no PDB 4BBN . "Nedd4 Hect-ub:ub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 224 no PDB 4BOS . "Structure Of Otud2 Otu Domain In Complex With Ubiquitin K11- Linked Peptide" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 225 no PDB 4BOZ . "Structure Of Otud2 Otu Domain In Complex With K11-linked Di Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 226 no PDB 4BVU . "Structure Of Shigella Effector Ospg In Complex With Host Ubch5c-ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 227 no PDB 4CXC . "Regulation Of The Mammalian Elongation Cycle By 40s Subunit Rolling: A Eukaryotic-specific Ribosome Rearrangement" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 228 no PDB 4CXD . "Regulation Of The Mammalian Elongation Cycle By 40s Subunit Rolling: A Eukaryotic-specific Ribosome Rearrangement" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 229 no PDB 4D5L . "Cryo-em Structures Of Ribosomal 80s Complexes With Termination Factors And Cricket Paralysis Virus Ires Reveal The Ires In The " . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 230 no PDB 4D61 . "Cryo-em Structures Of Ribosomal 80s Complexes With Termination Factors And Cricket Paralysis Virus Ires Reveal The Ires In The " . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 231 no PDB 4DDG . "Crystal Structure Of Human Otub1UBCH5B~UBUB" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 232 no PDB 4DDI . "Crystal Structure Of Human Otub1UBCH5B~UBUB" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 233 no PDB 4DHJ . "The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub Complex" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 234 no PDB 4DHZ . "The Structure Of HCEOTUB1-Ubiquitin Aldehyde-Ubc13~ub" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 235 no PDB 4FJV . "Crystal Structure Of Human Otubain2 And Ubiquitin Complex" . . . . . 100.00 86 100.00 100.00 9.86e-46 . . . . 18583 1 + 236 no PDB 4HXD . "Diversity Of Ubiquitin And Isg15 Specificity Amongst Nairoviruses Viral Ovarian Tumor Domain Proteases" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 237 no PDB 4I6N . "Crystal Structure Of Trichinella Spiralis Uch37 Catalytic Domain Bound To Ubiquitin Vinyl Methyl Ester" . . . . . 97.37 75 100.00 100.00 4.54e-44 . . . . 18583 1 + 238 no PDB 4IG7 . "Crystal Structure Of Trichinella Spiralis Uch37 Bound To Ubiquitin Vinyl Methyl Ester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 239 no PDB 4IUM . "Equine Arteritis Virus Papain-like Protease 2 (plp2) Covalently Bound To Ubiquitin" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 240 no PDB 4JIO . "Bro1 V Domain And Ubiquitin" . . . . . 100.00 76 98.68 98.68 4.85e-45 . . . . 18583 1 + 241 no PDB 4JQW . "Crystal Structure Of A Complex Of Nod1 Card And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 242 no PDB 4K1R . "Crystal Structure Of Schizosaccharomyces Pombe Sst2 Catalytic Domain And Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 243 no PDB 4K7S . "Crystal Structure Of Zn2-hub (human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 244 no PDB 4K7U . "Crystal Structure Of Zn2.3-hub (human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 245 no PDB 4K7W . "Crystal Structure Of Zn3-hub(human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 246 no PDB 4KSK . "Gumby/fam105b In Complex With Ubiquitin" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 247 no PDB 4KSL . "Gumby/fam105b In Complex With Linear Di-ubiquitin" . . . . . 100.00 156 100.00 100.00 6.34e-45 . . . . 18583 1 + 248 no PDB 4KZX . "Rabbit 40s Ribosomal Subunit In Complex With Eif1." . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 249 no PDB 4KZY . "Rabbit 40s Ribosomal Subunit In Complex With Eif1 And Eif1a." . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 250 no PDB 4KZZ . "Rabbit 40s Ribosomal Subunit In Complex With Mrna, Initiator Trna And Eif1a" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 251 no PDB 4LCD . "Structure Of An Rsp5xubxsna3 Complex: Mechanism Of Ubiquitin Ligation And Lysine Prioritization By A Hect E3" . . . . . 97.37 83 100.00 100.00 1.79e-44 . . . . 18583 1 + 252 no PDB 4LDT . "The Structure Of H/ceotub1-ubiquitin Aldehyde-ubch5b~ub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 253 no PDB 4LJO . "Structure Of An Active Ligase (hoip)/ubiquitin Transfer Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 254 no PDB 4LJP . "Structure Of An Active Ligase (hoip-h889a)/ubiquitin Transfer Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 255 no PDB 4M0W . "Crystal Structure Of Sars-cov Papain-like Protease C112s Mutant In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 256 no PDB 4MDK . "Cdc34-ubiquitin-cc0651 Complex" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 257 no PDB 4MM3 . "Crystal Structure Of Sars-cov Papain-like Protease Plpro In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 258 no PDB 4MSM . "Crystal Structure Of Schizosaccharomyces Pombe Amsh-like Protease Sst2 E286a Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 259 no PDB 4MSQ . "Crystal Structure Of Schizosaccharomyces Pombe Amsh-like Protease Sst2 Catalytic Domain Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 260 no PDB 4NQK . "Structure Of An Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 1.20e-45 . . . . 18583 1 + 261 no PDB 4NQL . "The Crystal Structure Of The Dub Domain Of Amsh Orthologue, Sst2 From S. Pombe, In Complex With Lysine 63-linked Diubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 262 no PDB 4P4H . "Caught-in-action Signaling Complex Of Rig-i 2card Domain And Mavs Card Domain" . . . . . 100.00 79 100.00 100.00 1.20e-45 . . . . 18583 1 + 263 no PDB 4PIG . "Crystal Structure Of The Ubiquitin K11s Mutant" . . . . . 100.00 76 98.68 98.68 2.81e-45 . . . . 18583 1 + 264 no PDB 4PIH . "X-ray Crystal Structure Of The K33s Mutant Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 2.81e-45 . . . . 18583 1 + 265 no PDB 4PIJ . "X-ray Crystal Structure Of The K11s/k63s Double Mutant Of Ubiquitin" . . . . . 98.68 75 97.33 97.33 7.90e-44 . . . . 18583 1 + 266 no PDB 4PQT . "Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Co-crystal Structures Of Enzyme With Substrate And" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 267 no PDB 4R62 . "Structure Of Rad6~ub" . . . . . 100.00 78 100.00 100.00 6.20e-46 . . . . 18583 1 + 268 no PDB 4RF0 . "Crystal Structure Of The Middle-east Respiratory Syndrome Coronavirus Papain-like Protease In Complex With Ubiquitin (space Gro" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 269 no PDB 4RF1 . "Crystal Structure Of The Middle-east Respiratory Syndrome Coronavirus Papain-like Protease In Complex With Ubiquitin (space Gro" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 270 no PDB 4S1Z . "Crystal Structure Of Trabid Nzf1 In Complex With K29 Linked Di- Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 271 no PDB 4S22 . "Crystal Structure Of K29 Linked Di-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 272 no PDB 4UEL . "Uch-l5 In Complex With Ubiquitin-propargyl Bound To The Rpn13 Deubad Domain" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 273 no PDB 4UF6 . "Uch-l5 In Complex With Ubiquitin-propargyl Bound To An Activating Fragment Of Ino80g" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 274 no PDB 4UN2 . "Crystal Structure Of The Uba Domain Of Dsk2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 275 no PDB 4UPX . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Pre-like State" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 276 no PDB 4UQ1 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Post-like State" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 277 no PDB 4UQ4 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Post-like State" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 278 no PDB 4UQ5 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Pre-like State" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 279 no PDB 4V3K . "Rnf38-ubch5b-ub Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 280 no PDB 4V3L . "Rnf38-ub-ubch5b-ub Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 281 no PDB 4W20 . "Structure Of The Mammalian 60s Ribosomal Subunit (this Entry Contains The Large Ribosomal Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 282 no PDB 4W22 . "Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 283 no PDB 4W23 . "Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Small Ribosomal Subunit)" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 284 no PDB 4W25 . "Structure Of The Idle Mammalian Ribosome-sec61 Complex (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 285 no PDB 4W27 . "Structure Of The Translating Mammalian Ribosome-sec61 Complex (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 286 no PDB 4W28 . "Structure Of The Translating Mammalian Ribosome-sec61 Complex (this Entry Contains The Small Ribosomal Subunit)" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 287 no PDB 4WHV . Rnf8/ubc13c87k~ub . . . . . 100.00 83 100.00 100.00 1.61e-45 . . . . 18583 1 + 288 no PDB 4WLR . "Crystal Structure Of Much37-hrpn13 Ctd-hub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 289 no PDB 4WUR . "The Crystal Structure Of The Mers-cov Papain-like Protease (c111s) With Human Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 290 no PDB 4WZP . "Ser65 Phosphorylated Ubiquitin, Major Conformation" . . . . . 100.00 76 98.68 98.68 4.64e-45 . . . . 18583 1 + 291 no PDB 4XKL . "Crystal Structure Of Ndp52 Zf2 In Complex With Mono-ubiquitin" . . . . . 100.00 80 100.00 100.00 1.02e-45 . . . . 18583 1 + 292 no PDB 4XOF . "Observing The Overall Rocking Motion Of A Protein In A Crystal - Orthorhombic Ubiquitin Crystals Without Zinc." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 293 no PDB 4XOK . "Observing The Overall Rocking Motion Of A Protein In A Crystal." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 294 no PDB 4XOL . "Observing The Overall Rocking Motion Of A Protein In A Crystal - Cubic Ubiquitin Crystals." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 295 no PDB 4XYZ . "Crystal Structure Of K33 Linked Di-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 296 no PDB 4Y1H . "Crystal Structure Of K33 Linked Tri-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 297 no PDB 4Z9S . "Non-covalent Assembly Of Monoubiquitin That Mimics K11 Poly-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 298 no PDB 4ZFR . "Catalytic Domain Of Sst2 F403a Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 299 no PDB 4ZFT . "Catalytic Domain Of Sst2 F403w Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 300 no PDB 4ZPZ . "Crystal Structure Of Semi-synthetic Ubiquitin With Phospho-ser65 And Ala46cys" . . . . . 100.00 76 97.37 97.37 1.81e-44 . . . . 18583 1 + 301 no PDB 5A5B . "Structure Of The 26s Proteasome-ubp6 Complex" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 302 no PDB 5AF4 . "Structure Of Lys33-linked Diub" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 303 no PDB 5AF5 . "Structure Of Lys33-linked Triub S.g. P 212121" . . . . . 96.05 73 98.63 100.00 5.42e-43 . . . . 18583 1 + 304 no PDB 5AF6 . "Structure Of Lys33-linked Diub Bound To Trabid Nzf1" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 305 no PDB 5AIT . "A Complex Of Of Rnf4-ring Domain, Ubev2, Ubc13-ub (isopeptide Crosslink)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 306 no PDB 5AIU . "A Complex Of Rnf4-ring Domain, Ubc13-ub (isopeptide Crosslink)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 307 no PDB 5CAW . "Structure Of Pediculus Humanus Parkin Bound To Phospho-ubiquitin" . . . . . 98.68 76 98.67 98.67 2.77e-44 . . . . 18583 1 + 308 no DBJ BAA03983 . "polyubiquitin [Rattus norvegicus]" . . . . . 100.00 305 100.00 100.00 3.25e-43 . . . . 18583 1 + 309 no DBJ BAA09860 . "polyubiquitin [Homo sapiens]" . . . . . 100.00 611 98.68 98.68 1.53e-40 . . . . 18583 1 + 310 no DBJ BAA11842 . "ubiquitin [Cavia porcellus]" . . . . . 100.00 311 100.00 100.00 3.52e-43 . . . . 18583 1 + 311 no DBJ BAA11843 . "ubiquitin extention protein [Cavia porcellus]" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 312 no DBJ BAA23486 . "polyubiquitin [Homo sapiens]" . . . . . 100.00 609 98.68 98.68 8.23e-41 . . . . 18583 1 + 313 no EMBL CAA25706 . "unnamed protein product [Saccharomyces cerevisiae]" . . . . . 50.00 191 100.00 100.00 4.38e-16 . . . . 18583 1 + 314 no EMBL CAA26488 . "unnamed protein product [Gallus gallus]" . . . . . 100.00 157 98.68 98.68 3.90e-44 . . . . 18583 1 + 315 no EMBL CAA28495 . "ubiquitin [Homo sapiens]" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 316 no EMBL CAA30183 . "unnamed protein product [Dictyostelium discoideum]" . . . . . 100.00 128 97.37 97.37 7.90e-44 . . . . 18583 1 + 317 no EMBL CAA30815 . "unnamed protein product [Cricetulus sp.]" . . . . . 93.42 223 100.00 100.00 5.43e-40 . . . . 18583 1 + 318 no GB AAA02769 . "polyprotein [Bovine viral diarrhea virus 1-Osloss]" . . . . . 98.68 3975 97.33 100.00 2.69e-39 . . . . 18583 1 + 319 no GB AAA28154 . "polyubiquitin [Caenorhabditis elegans]" . . . . . 100.00 838 97.37 98.68 1.06e-39 . . . . 18583 1 + 320 no GB AAA28997 . "ubiquitin [Drosophila melanogaster]" . . . . . 100.00 231 100.00 100.00 4.85e-44 . . . . 18583 1 + 321 no GB AAA28998 . "ubiquitin-hybrid protein precursor [Drosophila melanogaster]" . . . . . 100.00 156 100.00 100.00 1.42e-45 . . . . 18583 1 + 322 no GB AAA28999 . "ubiquitin, partial [Drosophila melanogaster]" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 323 no PIR I50437 . "polyubiquitin 4 - chicken [Gallus gallus]" . . . . . 100.00 305 100.00 100.00 3.25e-43 . . . . 18583 1 + 324 no PIR I51568 . "polyubiquitin - African clawed frog (fragment)" . . . . . 100.00 167 100.00 100.00 1.00e-44 . . . . 18583 1 + 325 no PIR I65237 . "ubiquitin / ribosomal protein L40, cytosolic [validated] - rat" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 326 no PIR JN0790 . "ubiquitin/ribosomal protein CEP52 fusion protein - Leishmania major" . . . . . 100.00 128 97.37 98.68 3.43e-45 . . . . 18583 1 + 327 no PIR S13928 . "ubiquitin precursor - chicken [Gallus gallus]" . . . . . 100.00 229 100.00 100.00 5.35e-44 . . . . 18583 1 + 328 no PRF 0412265A . ubiquitin . . . . . 98.68 75 98.67 98.67 1.80e-44 . . . . 18583 1 + 329 no PRF 1101405A . "ubiquitin precursor" . . . . . 50.00 191 100.00 100.00 4.33e-16 . . . . 18583 1 + 330 no PRF 1212243A . "ubiquitin S1" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 331 no PRF 1212243B . "ubiquitin S5" . . . . . 92.11 77 98.57 98.57 1.12e-40 . . . . 18583 1 + 332 no PRF 1212243C . "ubiquitin S3" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 333 no REF NP_001005123 . "ubiquitin-60S ribosomal protein L40 [Xenopus (Silurana) tropicalis]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 334 no REF NP_001006688 . "ubiquitin C [Xenopus (Silurana) tropicalis]" . . . . . 100.00 609 100.00 100.00 1.45e-41 . . . . 18583 1 + 335 no REF NP_001009117 . "polyubiquitin-B [Pan troglodytes]" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 336 no REF NP_001009202 . "polyubiquitin-B [Ovis aries]" . . . . . 100.00 305 98.68 100.00 5.72e-43 . . . . 18583 1 + 337 no REF NP_001009286 . "ubiquitin-60S ribosomal protein L40 [Ovis aries]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 338 no SP P0C273 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 339 no SP P0C275 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 340 no SP P0C276 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 341 no SP P0CG47 . "RecName: Full=Polyubiquitin-B; Contains: RecName: Full=Ubiquitin; Flags: Precursor" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 342 no SP P0CG48 . "RecName: Full=Polyubiquitin-C; Contains: RecName: Full=Ubiquitin; Flags: Precursor" . . . . . 100.00 685 100.00 100.00 2.13e-41 . . . . 18583 1 + 343 no TPD FAA00319 . "TPA: polyubiquitin [Cryptococcus neoformans var. neoformans B-3501A]" . . . . . 100.00 456 97.37 98.68 1.11e-40 . . . . 18583 1 + 344 no TPE CEL68433 . "TPA: ubiquitin / ribosomal protein CEP52 fusion protein, putative [Neospora caninum Liverpool]" . . . . . 100.00 129 98.68 100.00 1.60e-45 . . . . 18583 1 + 345 no TPE CEL70397 . "TPA: Ubiquitin, related [Neospora caninum Liverpool]" . . . . . 100.00 535 98.68 100.00 3.17e-41 . . . . 18583 1 + 346 no TPE CEL75964 . "TPA: ubiquitin / ribosomal protein CEP52 fusion protein, putative [Toxoplasma gondii VEG]" . . . . . 100.00 129 98.68 100.00 1.60e-45 . . . . 18583 1 + 347 no TPE CEL78064 . "TPA: polyubiquitin, putative [Toxoplasma gondii VEG]" . . . . . 100.00 307 98.68 100.00 1.16e-42 . . . . 18583 1 + 348 no TPG DAA18802 . "TPA: polyubiquitin [Bos taurus]" . . . . . 100.00 305 100.00 100.00 3.43e-43 . . . . 18583 1 + 349 no TPG DAA20663 . "TPA: ubiquitin C [Bos taurus]" . . . . . 98.68 314 98.67 100.00 1.30e-41 . . . . 18583 1 + 350 no TPG DAA20672 . "TPA: ubiquitin B-like [Bos taurus]" . . . . . 100.00 77 98.68 98.68 4.88e-45 . . . . 18583 1 + 351 no TPG DAA24675 . "TPA: 40S ribosomal protein S27a [Bos taurus]" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 352 no TPG DAA28295 . "TPA: ubiquitin and ribosomal protein L40 [Bos taurus]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + + stop_ + + loop_ + _Entity_comp_index.ID + _Entity_comp_index.Auth_seq_ID + _Entity_comp_index.Comp_ID + _Entity_comp_index.Comp_label + _Entity_comp_index.Entry_ID + _Entity_comp_index.Entity_ID + + 1 . MET . 18583 1 + 2 . GLN . 18583 1 + 3 . ILE . 18583 1 + 4 . PHE . 18583 1 + 5 . VAL . 18583 1 + 6 . LYS . 18583 1 + 7 . THR . 18583 1 + 8 . LEU . 18583 1 + 9 . THR . 18583 1 + 10 . GLY . 18583 1 + 11 . LYS . 18583 1 + 12 . THR . 18583 1 + 13 . ILE . 18583 1 + 14 . THR . 18583 1 + 15 . LEU . 18583 1 + 16 . GLU . 18583 1 + 17 . VAL . 18583 1 + 18 . GLU . 18583 1 + 19 . PRO . 18583 1 + 20 . SER . 18583 1 + 21 . ASP . 18583 1 + 22 . THR . 18583 1 + 23 . ILE . 18583 1 + 24 . GLU . 18583 1 + 25 . ASN . 18583 1 + 26 . VAL . 18583 1 + 27 . LYS . 18583 1 + 28 . ALA . 18583 1 + 29 . LYS . 18583 1 + 30 . ILE . 18583 1 + 31 . GLN . 18583 1 + 32 . ASP . 18583 1 + 33 . LYS . 18583 1 + 34 . GLU . 18583 1 + 35 . GLY . 18583 1 + 36 . ILE . 18583 1 + 37 . PRO . 18583 1 + 38 . PRO . 18583 1 + 39 . ASP . 18583 1 + 40 . GLN . 18583 1 + 41 . GLN . 18583 1 + 42 . ARG . 18583 1 + 43 . LEU . 18583 1 + 44 . ILE . 18583 1 + 45 . PHE . 18583 1 + 46 . ALA . 18583 1 + 47 . GLY . 18583 1 + 48 . LYS . 18583 1 + 49 . GLN . 18583 1 + 50 . LEU . 18583 1 + 51 . GLU . 18583 1 + 52 . ASP . 18583 1 + 53 . GLY . 18583 1 + 54 . ARG . 18583 1 + 55 . THR . 18583 1 + 56 . LEU . 18583 1 + 57 . SER . 18583 1 + 58 . ASP . 18583 1 + 59 . TYR . 18583 1 + 60 . ASN . 18583 1 + 61 . ILE . 18583 1 + 62 . GLN . 18583 1 + 63 . LYS . 18583 1 + 64 . GLU . 18583 1 + 65 . SER . 18583 1 + 66 . THR . 18583 1 + 67 . LEU . 18583 1 + 68 . HIS . 18583 1 + 69 . LEU . 18583 1 + 70 . VAL . 18583 1 + 71 . LEU . 18583 1 + 72 . ARG . 18583 1 + 73 . LEU . 18583 1 + 74 . ARG . 18583 1 + 75 . GLY . 18583 1 + 76 . GLY . 18583 1 + + stop_ + + loop_ + _Entity_poly_seq.Hetero + _Entity_poly_seq.Mon_ID + _Entity_poly_seq.Num + _Entity_poly_seq.Comp_index_ID + _Entity_poly_seq.Entry_ID + _Entity_poly_seq.Entity_ID + + . MET 1 1 18583 1 + . GLN 2 2 18583 1 + . ILE 3 3 18583 1 + . PHE 4 4 18583 1 + . VAL 5 5 18583 1 + . LYS 6 6 18583 1 + . THR 7 7 18583 1 + . LEU 8 8 18583 1 + . THR 9 9 18583 1 + . GLY 10 10 18583 1 + . LYS 11 11 18583 1 + . THR 12 12 18583 1 + . ILE 13 13 18583 1 + . THR 14 14 18583 1 + . LEU 15 15 18583 1 + . GLU 16 16 18583 1 + . VAL 17 17 18583 1 + . GLU 18 18 18583 1 + . PRO 19 19 18583 1 + . SER 20 20 18583 1 + . ASP 21 21 18583 1 + . THR 22 22 18583 1 + . ILE 23 23 18583 1 + . GLU 24 24 18583 1 + . ASN 25 25 18583 1 + . VAL 26 26 18583 1 + . LYS 27 27 18583 1 + . ALA 28 28 18583 1 + . LYS 29 29 18583 1 + . ILE 30 30 18583 1 + . GLN 31 31 18583 1 + . ASP 32 32 18583 1 + . LYS 33 33 18583 1 + . GLU 34 34 18583 1 + . GLY 35 35 18583 1 + . ILE 36 36 18583 1 + . PRO 37 37 18583 1 + . PRO 38 38 18583 1 + . ASP 39 39 18583 1 + . GLN 40 40 18583 1 + . GLN 41 41 18583 1 + . ARG 42 42 18583 1 + . LEU 43 43 18583 1 + . ILE 44 44 18583 1 + . PHE 45 45 18583 1 + . ALA 46 46 18583 1 + . GLY 47 47 18583 1 + . LYS 48 48 18583 1 + . GLN 49 49 18583 1 + . LEU 50 50 18583 1 + . GLU 51 51 18583 1 + . ASP 52 52 18583 1 + . GLY 53 53 18583 1 + . ARG 54 54 18583 1 + . THR 55 55 18583 1 + . LEU 56 56 18583 1 + . SER 57 57 18583 1 + . ASP 58 58 18583 1 + . TYR 59 59 18583 1 + . ASN 60 60 18583 1 + . ILE 61 61 18583 1 + . GLN 62 62 18583 1 + . LYS 63 63 18583 1 + . GLU 64 64 18583 1 + . SER 65 65 18583 1 + . THR 66 66 18583 1 + . LEU 67 67 18583 1 + . HIS 68 68 18583 1 + . LEU 69 69 18583 1 + . VAL 70 70 18583 1 + . LEU 71 71 18583 1 + . ARG 72 72 18583 1 + . LEU 73 73 18583 1 + . ARG 74 74 18583 1 + . GLY 75 75 18583 1 + . GLY 76 76 18583 1 + + stop_ + +save_ + + +save_entity_2 + _Entity.Sf_category entity + _Entity.Sf_framecode entity_2 + _Entity.Entry_ID 18583 + _Entity.ID 2 + _Entity.BMRB_code . + _Entity.Name gp78CUE + _Entity.Type polymer + _Entity.Polymer_common_type . + _Entity.Polymer_type polypeptide(L) + _Entity.Polymer_type_details . + _Entity.Polymer_strand_ID C + _Entity.Polymer_seq_one_letter_code_can . + _Entity.Polymer_seq_one_letter_code +; +SNSQLNAMAHQIQEMFPQVP +YHLVLQDLQLTRSVEITTDN +ILEGRIQVPFPT +; + _Entity.Target_identifier . + _Entity.Polymer_author_defined_seq . + _Entity.Polymer_author_seq_details . + _Entity.Ambiguous_conformational_states no + _Entity.Ambiguous_chem_comp_sites no + _Entity.Nstd_monomer no + _Entity.Nstd_chirality no + _Entity.Nstd_linkage no + _Entity.Nonpolymer_comp_ID . + _Entity.Nonpolymer_comp_label . + _Entity.Number_of_monomers 52 + _Entity.Number_of_nonpolymer_components . + _Entity.Paramagnetic no + _Entity.Thiol_state 'not present' + _Entity.Src_method man + _Entity.Parent_entity_ID . + _Entity.Fragment . + _Entity.Mutation . + _Entity.EC_number . + _Entity.Calc_isoelectric_point . + _Entity.Formula_weight 5966.808 + _Entity.Formula_weight_exptl . + _Entity.Formula_weight_exptl_meth . + _Entity.Details . + _Entity.DB_query_date . + _Entity.DB_query_revised_last_date 2015-01-30 + + loop_ + _Entity_db_link.Ordinal + _Entity_db_link.Author_supplied + _Entity_db_link.Database_code + _Entity_db_link.Accession_code + _Entity_db_link.Entry_mol_code + _Entity_db_link.Entry_mol_name + _Entity_db_link.Entry_experimental_method + _Entity_db_link.Entry_structure_resolution + _Entity_db_link.Entry_relation_type + _Entity_db_link.Entry_details + _Entity_db_link.Chimera_segment_ID + _Entity_db_link.Seq_query_to_submitted_percent + _Entity_db_link.Seq_subject_length + _Entity_db_link.Seq_identity + _Entity_db_link.Seq_positive + _Entity_db_link.Seq_homology_expectation_val + _Entity_db_link.Seq_align_begin + _Entity_db_link.Seq_align_end + _Entity_db_link.Seq_difference_details + _Entity_db_link.Seq_alignment_details + _Entity_db_link.Entry_ID + _Entity_db_link.Entity_ID + + 1 no BMRB 18581 . entity . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 2 no BMRB 18582 . gp78CUE . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 3 no BMRB 18584 . gp78CUE . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 4 no PDB 2EJS . "Solution Structure Of Ruh-076, A Human Cue Domain" . . . . . 96.15 58 100.00 100.00 2.71e-27 . . . . 18583 2 + 5 no PDB 2LVN . "Structure Of The Gp78 Cue Domain" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 6 no PDB 2LVO . "Structure Of The Gp78cue Domain Bound To Monubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 7 no PDB 2LVP . "Gp78cue Domain Bound To The Distal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 8 no PDB 2LVQ . "Gp78cue Domain Bound To The Proximal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 9 no PDB 4G3O . "Crystal Structure Of The Cue Domain Of The E3 Ubiquitin Ligase Amfr (Gp78)" . . . . . 84.62 58 97.73 97.73 9.44e-22 . . . . 18583 2 + 10 no DBJ BAE01277 . "unnamed protein product [Macaca fascicularis]" . . . . . 100.00 552 100.00 100.00 3.33e-26 . . . . 18583 2 + 11 no DBJ BAE34049 . "unnamed protein product [Mus musculus]" . . . . . 100.00 643 98.08 100.00 1.44e-25 . . . . 18583 2 + 12 no DBJ BAE41974 . "unnamed protein product [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 13 no DBJ BAK63135 . "autocrine motility factor receptor, isoform 2 [Pan troglodytes]" . . . . . 100.00 548 100.00 100.00 3.46e-26 . . . . 18583 2 + 14 no GB AAD56721 . "autocrine motility factor receptor [Mus musculus]" . . . . . 100.00 643 98.08 100.00 1.32e-25 . . . . 18583 2 + 15 no GB AAD56722 . "autocrine motility factor receptor [Homo sapiens]" . . . . . 100.00 643 100.00 100.00 8.27e-26 . . . . 18583 2 + 16 no GB AAH03256 . "Amfr protein, partial [Mus musculus]" . . . . . 100.00 244 98.08 100.00 4.16e-27 . . . . 18583 2 + 17 no GB AAH17043 . "AMFR protein, partial [Homo sapiens]" . . . . . 100.00 292 100.00 100.00 4.77e-27 . . . . 18583 2 + 18 no GB AAH34538 . "Autocrine motility factor receptor [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 19 no REF NP_001039439 . "E3 ubiquitin-protein ligase AMFR [Bos taurus]" . . . . . 100.00 645 100.00 100.00 7.86e-26 . . . . 18583 2 + 20 no REF NP_001135 . "E3 ubiquitin-protein ligase AMFR [Homo sapiens]" . . . . . 100.00 643 100.00 100.00 7.72e-26 . . . . 18583 2 + 21 no REF NP_001267243 . "E3 ubiquitin-protein ligase AMFR [Pan troglodytes]" . . . . . 100.00 548 100.00 100.00 3.46e-26 . . . . 18583 2 + 22 no REF NP_035917 . "E3 ubiquitin-protein ligase AMFR [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 23 no REF XP_001091030 . "PREDICTED: autocrine motility factor receptor, isoform 2 [Macaca mulatta]" . . . . . 100.00 552 100.00 100.00 3.20e-26 . . . . 18583 2 + 24 no SP Q9R049 . "RecName: Full=E3 ubiquitin-protein ligase AMFR; AltName: Full=Autocrine motility factor receptor; Short=AMF receptor [Mus muscu" . . . . . 100.00 643 98.08 100.00 1.44e-25 . . . . 18583 2 + 25 no SP Q9UKV5 . "RecName: Full=E3 ubiquitin-protein ligase AMFR; AltName: Full=Autocrine motility factor receptor; Short=AMF receptor; AltName: " . . . . . 100.00 643 100.00 100.00 7.72e-26 . . . . 18583 2 + 26 no TPG DAA20037 . "TPA: autocrine motility factor receptor [Bos taurus]" . . . . . 100.00 590 100.00 100.00 7.80e-26 . . . . 18583 2 + + stop_ + + loop_ + _Entity_comp_index.ID + _Entity_comp_index.Auth_seq_ID + _Entity_comp_index.Comp_ID + _Entity_comp_index.Comp_label + _Entity_comp_index.Entry_ID + _Entity_comp_index.Entity_ID + + 1 453 SER . 18583 2 + 2 454 ASN . 18583 2 + 3 455 SER . 18583 2 + 4 456 GLN . 18583 2 + 5 457 LEU . 18583 2 + 6 458 ASN . 18583 2 + 7 459 ALA . 18583 2 + 8 460 MET . 18583 2 + 9 461 ALA . 18583 2 + 10 462 HIS . 18583 2 + 11 463 GLN . 18583 2 + 12 464 ILE . 18583 2 + 13 465 GLN . 18583 2 + 14 466 GLU . 18583 2 + 15 467 MET . 18583 2 + 16 468 PHE . 18583 2 + 17 469 PRO . 18583 2 + 18 470 GLN . 18583 2 + 19 471 VAL . 18583 2 + 20 472 PRO . 18583 2 + 21 473 TYR . 18583 2 + 22 474 HIS . 18583 2 + 23 475 LEU . 18583 2 + 24 476 VAL . 18583 2 + 25 477 LEU . 18583 2 + 26 478 GLN . 18583 2 + 27 479 ASP . 18583 2 + 28 480 LEU . 18583 2 + 29 481 GLN . 18583 2 + 30 482 LEU . 18583 2 + 31 483 THR . 18583 2 + 32 484 ARG . 18583 2 + 33 485 SER . 18583 2 + 34 486 VAL . 18583 2 + 35 487 GLU . 18583 2 + 36 488 ILE . 18583 2 + 37 489 THR . 18583 2 + 38 490 THR . 18583 2 + 39 491 ASP . 18583 2 + 40 492 ASN . 18583 2 + 41 493 ILE . 18583 2 + 42 494 LEU . 18583 2 + 43 495 GLU . 18583 2 + 44 496 GLY . 18583 2 + 45 497 ARG . 18583 2 + 46 498 ILE . 18583 2 + 47 499 GLN . 18583 2 + 48 500 VAL . 18583 2 + 49 501 PRO . 18583 2 + 50 502 PHE . 18583 2 + 51 503 PRO . 18583 2 + 52 504 THR . 18583 2 + + stop_ + + loop_ + _Entity_poly_seq.Hetero + _Entity_poly_seq.Mon_ID + _Entity_poly_seq.Num + _Entity_poly_seq.Comp_index_ID + _Entity_poly_seq.Entry_ID + _Entity_poly_seq.Entity_ID + + . SER 1 1 18583 2 + . ASN 2 2 18583 2 + . SER 3 3 18583 2 + . GLN 4 4 18583 2 + . LEU 5 5 18583 2 + . ASN 6 6 18583 2 + . ALA 7 7 18583 2 + . MET 8 8 18583 2 + . ALA 9 9 18583 2 + . HIS 10 10 18583 2 + . GLN 11 11 18583 2 + . ILE 12 12 18583 2 + . GLN 13 13 18583 2 + . GLU 14 14 18583 2 + . MET 15 15 18583 2 + . PHE 16 16 18583 2 + . PRO 17 17 18583 2 + . GLN 18 18 18583 2 + . VAL 19 19 18583 2 + . PRO 20 20 18583 2 + . TYR 21 21 18583 2 + . HIS 22 22 18583 2 + . LEU 23 23 18583 2 + . VAL 24 24 18583 2 + . LEU 25 25 18583 2 + . GLN 26 26 18583 2 + . ASP 27 27 18583 2 + . LEU 28 28 18583 2 + . GLN 29 29 18583 2 + . LEU 30 30 18583 2 + . THR 31 31 18583 2 + . ARG 32 32 18583 2 + . SER 33 33 18583 2 + . VAL 34 34 18583 2 + . GLU 35 35 18583 2 + . ILE 36 36 18583 2 + . THR 37 37 18583 2 + . THR 38 38 18583 2 + . ASP 39 39 18583 2 + . ASN 40 40 18583 2 + . ILE 41 41 18583 2 + . LEU 42 42 18583 2 + . GLU 43 43 18583 2 + . GLY 44 44 18583 2 + . ARG 45 45 18583 2 + . ILE 46 46 18583 2 + . GLN 47 47 18583 2 + . VAL 48 48 18583 2 + . PRO 49 49 18583 2 + . PHE 50 50 18583 2 + . PRO 51 51 18583 2 + . THR 52 52 18583 2 + + stop_ + +save_ + + + #################### + # Natural source # + #################### + +save_natural_source + _Entity_natural_src_list.Sf_category natural_source + _Entity_natural_src_list.Sf_framecode natural_source + _Entity_natural_src_list.Entry_ID 18583 + _Entity_natural_src_list.ID 1 + + loop_ + _Entity_natural_src.ID + _Entity_natural_src.Entity_ID + _Entity_natural_src.Entity_label + _Entity_natural_src.Entity_chimera_segment_ID + _Entity_natural_src.NCBI_taxonomy_ID + _Entity_natural_src.Type + _Entity_natural_src.Common + _Entity_natural_src.Organism_name_scientific + _Entity_natural_src.Organism_name_common + _Entity_natural_src.Organism_acronym + _Entity_natural_src.ICTVdb_decimal_code + _Entity_natural_src.Superkingdom + _Entity_natural_src.Kingdom + _Entity_natural_src.Genus + _Entity_natural_src.Species + _Entity_natural_src.Strain + _Entity_natural_src.Variant + _Entity_natural_src.Subvariant + _Entity_natural_src.Organ + _Entity_natural_src.Tissue + _Entity_natural_src.Tissue_fraction + _Entity_natural_src.Cell_line + _Entity_natural_src.Cell_type + _Entity_natural_src.ATCC_number + _Entity_natural_src.Organelle + _Entity_natural_src.Cellular_location + _Entity_natural_src.Fragment + _Entity_natural_src.Fraction + _Entity_natural_src.Secretion + _Entity_natural_src.Plasmid + _Entity_natural_src.Plasmid_details + _Entity_natural_src.Gene_mnemonic + _Entity_natural_src.Dev_stage + _Entity_natural_src.Details + _Entity_natural_src.Citation_ID + _Entity_natural_src.Citation_label + _Entity_natural_src.Entry_ID + _Entity_natural_src.Entity_natural_src_list_ID + + 1 1 $entity_1 . 9606 organism . 'Homo sapiens' Human . . Eukaryota Metazoa Homo sapiens . . . . . . . . . . . . . . . . . . . . . 18583 1 + 2 2 $entity_2 . 9606 organism . 'Homo sapiens' Human . . Eukaryota Metazoa Homo sapiens . . . . . . . . . . . . . . . . . . . . . 18583 1 + + stop_ + +save_ + + + ######################### + # Experimental source # + ######################### + +save_experimental_source + _Entity_experimental_src_list.Sf_category experimental_source + _Entity_experimental_src_list.Sf_framecode experimental_source + _Entity_experimental_src_list.Entry_ID 18583 + _Entity_experimental_src_list.ID 1 + + loop_ + _Entity_experimental_src.ID + _Entity_experimental_src.Entity_ID + _Entity_experimental_src.Entity_label + _Entity_experimental_src.Entity_chimera_segment_ID + _Entity_experimental_src.Production_method + _Entity_experimental_src.Host_org_scientific_name + _Entity_experimental_src.Host_org_name_common + _Entity_experimental_src.Host_org_details + _Entity_experimental_src.Host_org_NCBI_taxonomy_ID + _Entity_experimental_src.Host_org_genus + _Entity_experimental_src.Host_org_species + _Entity_experimental_src.Host_org_strain + _Entity_experimental_src.Host_org_variant + _Entity_experimental_src.Host_org_subvariant + _Entity_experimental_src.Host_org_organ + _Entity_experimental_src.Host_org_tissue + _Entity_experimental_src.Host_org_tissue_fraction + _Entity_experimental_src.Host_org_cell_line + _Entity_experimental_src.Host_org_cell_type + _Entity_experimental_src.Host_org_cellular_location + _Entity_experimental_src.Host_org_organelle + _Entity_experimental_src.Host_org_gene + _Entity_experimental_src.Host_org_culture_collection + _Entity_experimental_src.Host_org_ATCC_number + _Entity_experimental_src.Vector_type + _Entity_experimental_src.PDBview_host_org_vector_name + _Entity_experimental_src.PDBview_plasmid_name + _Entity_experimental_src.Vector_name + _Entity_experimental_src.Vector_details + _Entity_experimental_src.Vendor_name + _Entity_experimental_src.Host_org_dev_stage + _Entity_experimental_src.Details + _Entity_experimental_src.Citation_ID + _Entity_experimental_src.Citation_label + _Entity_experimental_src.Entry_ID + _Entity_experimental_src.Entity_experimental_src_list_ID + + 1 1 $entity_1 . 'recombinant technology' 'Escherichia coli' . . . Escherichia coli . . . . . . . . . . . . . . . . pET3a . . . . . . 18583 1 + 2 2 $entity_2 . 'recombinant technology' 'Escherichia coli' . . . Escherichia coli . . . . . . . . . . . . . . . . pET3a . . . . . . 18583 1 + + stop_ + +save_ + + +##################################### +# Sample contents and methodology # +##################################### + + ######################## + # Sample description # + ######################## + +save_sample_1 + _Sample.Sf_category sample + _Sample.Sf_framecode sample_1 + _Sample.Entry_ID 18583 + _Sample.ID 1 + _Sample.Type solution + _Sample.Sub_type . + _Sample.Details +; +50 mM Tris pH 7.2 +50mM NaCl +; + _Sample.Aggregate_sample_number . + _Sample.Solvent_system '90% H2O/10% D2O' + _Sample.Preparation_date . + _Sample.Preparation_expiration_date . + _Sample.Polycrystallization_protocol . + _Sample.Single_crystal_protocol . + _Sample.Crystal_grow_apparatus . + _Sample.Crystal_grow_atmosphere . + _Sample.Crystal_grow_details . + _Sample.Crystal_grow_method . + _Sample.Crystal_grow_method_cit_ID . + _Sample.Crystal_grow_pH . + _Sample.Crystal_grow_pH_range . + _Sample.Crystal_grow_pressure . + _Sample.Crystal_grow_pressure_esd . + _Sample.Crystal_grow_seeding . + _Sample.Crystal_grow_seeding_cit_ID . + _Sample.Crystal_grow_temp . + _Sample.Crystal_grow_temp_details . + _Sample.Crystal_grow_temp_esd . + _Sample.Crystal_grow_time . + _Sample.Oriented_sample_prep_protocol . + _Sample.Lyophilization_cryo_protectant . + _Sample.Storage_protocol . + + loop_ + _Sample_component.ID + _Sample_component.Mol_common_name + _Sample_component.Isotopic_labeling + _Sample_component.Assembly_ID + _Sample_component.Assembly_label + _Sample_component.Entity_ID + _Sample_component.Entity_label + _Sample_component.Product_ID + _Sample_component.Type + _Sample_component.Concentration_val + _Sample_component.Concentration_val_min + _Sample_component.Concentration_val_max + _Sample_component.Concentration_val_units + _Sample_component.Concentration_val_err + _Sample_component.Vendor + _Sample_component.Vendor_product_name + _Sample_component.Vendor_product_code + _Sample_component.Entry_ID + _Sample_component.Sample_ID + + 1 TRIS 'natural abundance' . . . . . . 50 . . mM . . . . 18583 1 + 2 'sodium chloride' 'natural abundance' . . . . . . 50 . . mM . . . . 18583 1 + 3 H2O 'natural abundance' . . . . . . 90 . . % . . . . 18583 1 + 4 D2O 'natural abundance' . . . . . . 10 . . % . . . . 18583 1 + + stop_ + +save_ + + +####################### +# Sample conditions # +####################### + +save_sample_conditions_1 + _Sample_condition_list.Sf_category sample_conditions + _Sample_condition_list.Sf_framecode sample_conditions_1 + _Sample_condition_list.Entry_ID 18583 + _Sample_condition_list.ID 1 + _Sample_condition_list.Details . + + loop_ + _Sample_condition_variable.Type + _Sample_condition_variable.Val + _Sample_condition_variable.Val_err + _Sample_condition_variable.Val_units + _Sample_condition_variable.Entry_ID + _Sample_condition_variable.Sample_condition_list_ID + + pH 7.2 . pH 18583 1 + pressure 1 . atm 18583 1 + temperature 298 . K 18583 1 + + stop_ + +save_ + + +############################ +# Computer software used # +############################ + +save_SPARKY + _Software.Sf_category software + _Software.Sf_framecode SPARKY + _Software.Entry_ID 18583 + _Software.ID 1 + _Software.Name SPARKY + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + Goddard . . 18583 1 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + 'chemical shift assignment' 18583 1 + 'peak picking' 18583 1 + + stop_ + +save_ + + +save_NMRPipe + _Software.Sf_category software + _Software.Sf_framecode NMRPipe + _Software.Entry_ID 18583 + _Software.ID 2 + _Software.Name NMRPipe + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . 18583 2 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + processing 18583 2 + + stop_ + +save_ + + +save_CNS + _Software.Sf_category software + _Software.Sf_framecode CNS + _Software.Entry_ID 18583 + _Software.ID 3 + _Software.Name CNS + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + 'Alexandre Bonvin' . . 18583 3 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + 'structure solution' 18583 3 + + stop_ + +save_ + + +######################### +# Experimental detail # +######################### + + ################################## + # NMR Spectrometer definitions # + ################################## + +save_spectrometer_1 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_1 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 1 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Bruker + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 600 + +save_ + + +save_spectrometer_2 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_2 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 2 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Bruker + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 700 + +save_ + + +save_spectrometer_3 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_3 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 3 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Varian + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 600 + +save_ + + +save_spectrometer_4 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_4 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 4 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Varian + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 800 + +save_ + + +save_NMR_spectrometer_list + _NMR_spectrometer_list.Sf_category NMR_spectrometer_list + _NMR_spectrometer_list.Sf_framecode NMR_spectrometer_list + _NMR_spectrometer_list.Entry_ID 18583 + _NMR_spectrometer_list.ID 1 + + loop_ + _NMR_spectrometer_view.ID + _NMR_spectrometer_view.Name + _NMR_spectrometer_view.Manufacturer + _NMR_spectrometer_view.Model + _NMR_spectrometer_view.Serial_number + _NMR_spectrometer_view.Field_strength + _NMR_spectrometer_view.Details + _NMR_spectrometer_view.Citation_ID + _NMR_spectrometer_view.Citation_label + _NMR_spectrometer_view.Entry_ID + _NMR_spectrometer_view.NMR_spectrometer_list_ID + + 1 spectrometer_1 Bruker INOVA . 600 . . . 18583 1 + 2 spectrometer_2 Bruker INOVA . 700 . . . 18583 1 + 3 spectrometer_3 Varian INOVA . 600 . . . 18583 1 + 4 spectrometer_4 Varian INOVA . 800 . . . 18583 1 + + stop_ + +save_ + + + ############################# + # NMR applied experiments # + ############################# + +save_experiment_list + _Experiment_list.Sf_category experiment_list + _Experiment_list.Sf_framecode experiment_list + _Experiment_list.Entry_ID 18583 + _Experiment_list.ID 1 + _Experiment_list.Details . + + loop_ + _Experiment.ID + _Experiment.Name + _Experiment.Raw_data_flag + _Experiment.NMR_spec_expt_ID + _Experiment.NMR_spec_expt_label + _Experiment.MS_expt_ID + _Experiment.MS_expt_label + _Experiment.SAXS_expt_ID + _Experiment.SAXS_expt_label + _Experiment.FRET_expt_ID + _Experiment.FRET_expt_label + _Experiment.EMR_expt_ID + _Experiment.EMR_expt_label + _Experiment.Sample_ID + _Experiment.Sample_label + _Experiment.Sample_state + _Experiment.Sample_volume + _Experiment.Sample_volume_units + _Experiment.Sample_condition_list_ID + _Experiment.Sample_condition_list_label + _Experiment.Sample_spinning_rate + _Experiment.Sample_angle + _Experiment.NMR_tube_type + _Experiment.NMR_spectrometer_ID + _Experiment.NMR_spectrometer_label + _Experiment.NMR_spectrometer_probe_ID + _Experiment.NMR_spectrometer_probe_label + _Experiment.NMR_spectral_processing_ID + _Experiment.NMR_spectral_processing_label + _Experiment.Mass_spectrometer_ID + _Experiment.Mass_spectrometer_label + _Experiment.Xray_instrument_ID + _Experiment.Xray_instrument_label + _Experiment.Fluorescence_instrument_ID + _Experiment.Fluorescence_instrument_label + _Experiment.EMR_instrument_ID + _Experiment.EMR_instrument_label + _Experiment.Chromatographic_system_ID + _Experiment.Chromatographic_system_label + _Experiment.Chromatographic_column_ID + _Experiment.Chromatographic_column_label + _Experiment.Entry_ID + _Experiment.Experiment_list_ID + + 1 '2D 1H-15N HSQC' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 2 '2D 1H-13C HSQC' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 3 '3D HNCO' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 4 '3D CBCA(CO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 5 '3D C(CO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 6 '3D H(CCO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 7 '3D HNCACB' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 8 '2D 1H-13C HSQC aromatic' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 9 '3D 1H-15N NOESY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + + stop_ + +save_ + + +#################### +# NMR parameters # +#################### + + ############################## + # Assigned chemical shifts # + ############################## + + ################################ + # Chemical shift referencing # + ################################ + +save_chemical_shift_reference_1 + _Chem_shift_reference.Sf_category chem_shift_reference + _Chem_shift_reference.Sf_framecode chemical_shift_reference_1 + _Chem_shift_reference.Entry_ID 18583 + _Chem_shift_reference.ID 1 + _Chem_shift_reference.Details . + + loop_ + _Chem_shift_ref.Atom_type + _Chem_shift_ref.Atom_isotope_number + _Chem_shift_ref.Mol_common_name + _Chem_shift_ref.Atom_group + _Chem_shift_ref.Concentration_val + _Chem_shift_ref.Concentration_units + _Chem_shift_ref.Solvent + _Chem_shift_ref.Rank + _Chem_shift_ref.Chem_shift_units + _Chem_shift_ref.Chem_shift_val + _Chem_shift_ref.Ref_method + _Chem_shift_ref.Ref_type + _Chem_shift_ref.Indirect_shift_ratio + _Chem_shift_ref.External_ref_loc + _Chem_shift_ref.External_ref_sample_geometry + _Chem_shift_ref.External_ref_axis + _Chem_shift_ref.Indirect_shift_ratio_cit_ID + _Chem_shift_ref.Indirect_shift_ratio_cit_label + _Chem_shift_ref.Ref_correction_type + _Chem_shift_ref.Correction_val + _Chem_shift_ref.Correction_val_cit_ID + _Chem_shift_ref.Correction_val_cit_label + _Chem_shift_ref.Entry_ID + _Chem_shift_ref.Chem_shift_reference_ID + + C 13 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.251449530 . . . . . . . . . 18583 1 + H 1 DSS 'methyl protons' . . . . ppm 0.00 internal direct 1.000000000 . . . . . . . . . 18583 1 + N 15 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.101329118 . . . . . . . . . 18583 1 + P 31 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.404808636 . . . . . . . . . 18583 1 + + stop_ + +save_ + + + ################################### + # Assigned chemical shift lists # + ################################### + +################################################################### +# Chemical Shift Ambiguity Index Value Definitions # +# # +# The values other than 1 are used for those atoms with different # +# chemical shifts that cannot be assigned to stereospecific atoms # +# or to specific residues or chains. # +# # +# Index Value Definition # +# # +# 1 Unique (including isolated methyl protons, # +# geminal atoms, and geminal methyl # +# groups with identical chemical shifts) # +# (e.g. ILE HD11, HD12, HD13 protons) # +# 2 Ambiguity of geminal atoms or geminal methyl # +# proton groups (e.g. ASP HB2 and HB3 # +# protons, LEU CD1 and CD2 carbons, or # +# LEU HD11, HD12, HD13 and HD21, HD22, # +# HD23 methyl protons) # +# 3 Aromatic atoms on opposite sides of # +# symmetrical rings (e.g. TYR HE1 and HE2 # +# protons) # +# 4 Intraresidue ambiguities (e.g. LYS HG and # +# HD protons or TRP HZ2 and HZ3 protons) # +# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # +# 6 Intermolecular ambiguities (e.g. ASP 31 CA # +# in monomer 1 and ASP 31 CA in monomer 2 # +# of an asymmetrical homodimer, duplex # +# DNA assignments, or other assignments # +# that may apply to atoms in one or more # +# molecule in the molecular assembly) # +# 9 Ambiguous, specific ambiguity not defined # +# # +################################################################### +save_gp78CUE_amides_in_gp78-K48Ub2 + _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts + _Assigned_chem_shift_list.Sf_framecode gp78CUE_amides_in_gp78-K48Ub2 + _Assigned_chem_shift_list.Entry_ID 18583 + _Assigned_chem_shift_list.ID 1 + _Assigned_chem_shift_list.Sample_condition_list_ID 1 + _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 + _Assigned_chem_shift_list.Chem_shift_reference_ID 1 + _Assigned_chem_shift_list.Chem_shift_reference_label $chemical_shift_reference_1 + _Assigned_chem_shift_list.Chem_shift_1H_err 0.05 + _Assigned_chem_shift_list.Chem_shift_13C_err 0.5 + _Assigned_chem_shift_list.Chem_shift_15N_err 0.2 + _Assigned_chem_shift_list.Chem_shift_31P_err . + _Assigned_chem_shift_list.Chem_shift_2H_err . + _Assigned_chem_shift_list.Chem_shift_19F_err . + _Assigned_chem_shift_list.Error_derivation_method . + _Assigned_chem_shift_list.Details . + _Assigned_chem_shift_list.Text_data_format . + _Assigned_chem_shift_list.Text_data . + + loop_ + _Chem_shift_experiment.Experiment_ID + _Chem_shift_experiment.Experiment_name + _Chem_shift_experiment.Sample_ID + _Chem_shift_experiment.Sample_label + _Chem_shift_experiment.Sample_state + _Chem_shift_experiment.Entry_ID + _Chem_shift_experiment.Assigned_chem_shift_list_ID + + 1 '2D 1H-15N HSQC' . . . 18583 1 + 4 '3D CBCA(CO)NH' . . . 18583 1 + 7 '3D HNCACB' . . . 18583 1 + + stop_ + + loop_ + _Atom_chem_shift.ID + _Atom_chem_shift.Assembly_atom_ID + _Atom_chem_shift.Entity_assembly_ID + _Atom_chem_shift.Entity_ID + _Atom_chem_shift.Comp_index_ID + _Atom_chem_shift.Seq_ID + _Atom_chem_shift.Comp_ID + _Atom_chem_shift.Atom_ID + _Atom_chem_shift.Atom_type + _Atom_chem_shift.Atom_isotope_number + _Atom_chem_shift.Val + _Atom_chem_shift.Val_err + _Atom_chem_shift.Assign_fig_of_merit + _Atom_chem_shift.Ambiguity_code + _Atom_chem_shift.Occupancy + _Atom_chem_shift.Resonance_ID + _Atom_chem_shift.Auth_entity_assembly_ID + _Atom_chem_shift.Auth_asym_ID + _Atom_chem_shift.Auth_seq_ID + _Atom_chem_shift.Auth_comp_ID + _Atom_chem_shift.Auth_atom_ID + _Atom_chem_shift.Details + _Atom_chem_shift.Entry_ID + _Atom_chem_shift.Assigned_chem_shift_list_ID + + 1 . 1 1 2 2 GLN H H 1 8.98 0.05 . 1 . . . A 2 GLN H . 18583 1 + 2 . 1 1 2 2 GLN N N 15 122.96 0.20 . 1 . . . A 2 GLN N . 18583 1 + 3 . 1 1 3 3 ILE H H 1 8.27 0.05 . 1 . . . A 3 ILE H . 18583 1 + 4 . 1 1 3 3 ILE N N 15 114.84 0.20 . 1 . . . A 3 ILE N . 18583 1 + 5 . 1 1 4 4 PHE H H 1 8.56 0.05 . 1 . . . A 4 PHE H . 18583 1 + 6 . 1 1 4 4 PHE N N 15 118.78 0.20 . 1 . . . A 4 PHE N . 18583 1 + 7 . 1 1 5 5 VAL H H 1 9.35 0.05 . 1 . . . A 5 VAL H . 18583 1 + 8 . 1 1 5 5 VAL N N 15 120.88 0.20 . 1 . . . A 5 VAL N . 18583 1 + 9 . 1 1 6 6 LYS H H 1 9.05 0.05 . 1 . . . A 6 LYS H . 18583 1 + 10 . 1 1 6 6 LYS N N 15 128.64 0.20 . 1 . . . A 6 LYS N . 18583 1 + 11 . 1 1 7 7 THR H H 1 8.72 0.05 . 1 . . . A 7 THR H . 18583 1 + 12 . 1 1 7 7 THR N N 15 115.08 0.20 . 1 . . . A 7 THR N . 18583 1 + 13 . 1 1 8 8 LEU H H 1 9.34 0.05 . 1 . . . A 8 LEU H . 18583 1 + 14 . 1 1 8 8 LEU N N 15 121.97 0.20 . 1 . . . A 8 LEU N . 18583 1 + 15 . 1 1 9 9 THR H H 1 7.65 0.05 . 1 . . . A 9 THR H . 18583 1 + 16 . 1 1 9 9 THR N N 15 105.77 0.20 . 1 . . . A 9 THR N . 18583 1 + 17 . 1 1 10 10 GLY H H 1 7.82 0.05 . 1 . . . A 10 GLY H . 18583 1 + 18 . 1 1 10 10 GLY N N 15 109.42 0.20 . 1 . . . A 10 GLY N . 18583 1 + 19 . 1 1 11 11 LYS H H 1 7.33 0.05 . 1 . . . A 11 LYS H . 18583 1 + 20 . 1 1 11 11 LYS N N 15 122.48 0.20 . 1 . . . A 11 LYS N . 18583 1 + 21 . 1 1 12 12 THR H H 1 8.66 0.05 . 1 . . . A 12 THR H . 18583 1 + 22 . 1 1 12 12 THR N N 15 120.93 0.20 . 1 . . . A 12 THR N . 18583 1 + 23 . 1 1 13 13 ILE H H 1 9.72 0.05 . 1 . . . A 13 ILE H . 18583 1 + 24 . 1 1 13 13 ILE N N 15 129.80 0.20 . 1 . . . A 13 ILE N . 18583 1 + 25 . 1 1 14 14 THR H H 1 8.81 0.05 . 1 . . . A 14 THR H . 18583 1 + 26 . 1 1 14 14 THR N N 15 123.06 0.20 . 1 . . . A 14 THR N . 18583 1 + 27 . 1 1 15 15 LEU H H 1 8.68 0.05 . 1 . . . A 15 LEU H . 18583 1 + 28 . 1 1 15 15 LEU N N 15 125.43 0.20 . 1 . . . A 15 LEU N . 18583 1 + 29 . 1 1 16 16 GLU H H 1 8.13 0.05 . 1 . . . A 16 GLU H . 18583 1 + 30 . 1 1 16 16 GLU N N 15 122.68 0.20 . 1 . . . A 16 GLU N . 18583 1 + 31 . 1 1 17 17 VAL H H 1 8.96 0.05 . 1 . . . A 17 VAL H . 18583 1 + 32 . 1 1 17 17 VAL N N 15 117.75 0.20 . 1 . . . A 17 VAL N . 18583 1 + 33 . 1 1 18 18 GLU H H 1 8.65 0.05 . 1 . . . A 18 GLU H . 18583 1 + 34 . 1 1 18 18 GLU N N 15 119.32 0.20 . 1 . . . A 18 GLU N . 18583 1 + 35 . 1 1 20 20 SER H H 1 7.03 0.05 . 1 . . . A 20 SER H . 18583 1 + 36 . 1 1 20 20 SER N N 15 103.43 0.20 . 1 . . . A 20 SER N . 18583 1 + 37 . 1 1 21 21 ASP H H 1 8.08 0.05 . 1 . . . A 21 ASP H . 18583 1 + 38 . 1 1 21 21 ASP N N 15 124.19 0.20 . 1 . . . A 21 ASP N . 18583 1 + 39 . 1 1 22 22 THR H H 1 7.89 0.05 . 1 . . . A 22 THR H . 18583 1 + 40 . 1 1 22 22 THR N N 15 109.14 0.20 . 1 . . . A 22 THR N . 18583 1 + 41 . 1 1 23 23 ILE H H 1 8.56 0.05 . 1 . . . A 23 ILE H . 18583 1 + 42 . 1 1 23 23 ILE N N 15 121.79 0.20 . 1 . . . A 23 ILE N . 18583 1 + 43 . 1 1 24 24 GLU H H 1 8.48 0.05 . 1 . . . A 24 GLU H . 18583 1 + 44 . 1 1 24 24 GLU N N 15 121.73 0.20 . 1 . . . A 24 GLU N . 18583 1 + 45 . 1 1 25 25 ASN H H 1 7.95 0.05 . 1 . . . A 25 ASN H . 18583 1 + 46 . 1 1 25 25 ASN N N 15 121.25 0.20 . 1 . . . A 25 ASN N . 18583 1 + 47 . 1 1 26 26 VAL H H 1 8.16 0.05 . 1 . . . A 26 VAL H . 18583 1 + 48 . 1 1 26 26 VAL N N 15 122.46 0.20 . 1 . . . A 26 VAL N . 18583 1 + 49 . 1 1 27 27 LYS H H 1 8.53 0.05 . 1 . . . A 27 LYS H . 18583 1 + 50 . 1 1 27 27 LYS N N 15 119.23 0.20 . 1 . . . A 27 LYS N . 18583 1 + 51 . 1 1 28 28 ALA H H 1 7.99 0.05 . 1 . . . A 28 ALA H . 18583 1 + 52 . 1 1 28 28 ALA N N 15 123.09 0.20 . 1 . . . A 28 ALA N . 18583 1 + 53 . 1 1 29 29 LYS H H 1 7.93 0.05 . 1 . . . A 29 LYS H . 18583 1 + 54 . 1 1 29 29 LYS N N 15 120.64 0.20 . 1 . . . A 29 LYS N . 18583 1 + 55 . 1 1 30 30 ILE H H 1 8.29 0.05 . 1 . . . A 30 ILE H . 18583 1 + 56 . 1 1 30 30 ILE N N 15 121.76 0.20 . 1 . . . A 30 ILE N . 18583 1 + 57 . 1 1 31 31 GLN H H 1 8.53 0.05 . 1 . . . A 31 GLN H . 18583 1 + 58 . 1 1 31 31 GLN N N 15 123.81 0.20 . 1 . . . A 31 GLN N . 18583 1 + 59 . 1 1 32 32 ASP H H 1 8.12 0.05 . 1 . . . A 32 ASP H . 18583 1 + 60 . 1 1 32 32 ASP N N 15 120.19 0.20 . 1 . . . A 32 ASP N . 18583 1 + 61 . 1 1 33 33 LYS H H 1 7.48 0.05 . 1 . . . A 33 LYS H . 18583 1 + 62 . 1 1 33 33 LYS N N 15 115.87 0.20 . 1 . . . A 33 LYS N . 18583 1 + 63 . 1 1 34 34 GLU H H 1 8.71 0.05 . 1 . . . A 34 GLU H . 18583 1 + 64 . 1 1 34 34 GLU N N 15 114.03 0.20 . 1 . . . A 34 GLU N . 18583 1 + 65 . 1 1 36 36 ILE H H 1 6.12 0.05 . 1 . . . A 36 ILE H . 18583 1 + 66 . 1 1 36 36 ILE N N 15 120.80 0.20 . 1 . . . A 36 ILE N . 18583 1 + 67 . 1 1 39 39 ASP H H 1 8.57 0.05 . 1 . . . A 39 ASP H . 18583 1 + 68 . 1 1 39 39 ASP N N 15 113.90 0.20 . 1 . . . A 39 ASP N . 18583 1 + 69 . 1 1 40 40 GLN H H 1 7.80 0.05 . 1 . . . A 40 GLN H . 18583 1 + 70 . 1 1 40 40 GLN N N 15 116.92 0.20 . 1 . . . A 40 GLN N . 18583 1 + 71 . 1 1 41 41 GLN H H 1 7.52 0.05 . 1 . . . A 41 GLN H . 18583 1 + 72 . 1 1 41 41 GLN N N 15 117.92 0.20 . 1 . . . A 41 GLN N . 18583 1 + 73 . 1 1 43 43 LEU H H 1 8.81 0.05 . 1 . . . A 43 LEU H . 18583 1 + 74 . 1 1 43 43 LEU N N 15 123.75 0.20 . 1 . . . A 43 LEU N . 18583 1 + 75 . 1 1 44 44 ILE H H 1 9.27 0.05 . 1 . . . A 44 ILE H . 18583 1 + 76 . 1 1 44 44 ILE N N 15 123.21 0.20 . 1 . . . A 44 ILE N . 18583 1 + 77 . 1 1 45 45 PHE H H 1 8.82 0.05 . 1 . . . A 45 PHE H . 18583 1 + 78 . 1 1 45 45 PHE N N 15 124.80 0.20 . 1 . . . A 45 PHE N . 18583 1 + 79 . 1 1 46 46 ALA H H 1 8.72 0.05 . 1 . . . A 46 ALA H . 18583 1 + 80 . 1 1 46 46 ALA N N 15 133.01 0.20 . 1 . . . A 46 ALA N . 18583 1 + 81 . 1 1 48 48 LYS H H 1 8.56 0.05 . 1 . . . A 48 LYS H . 18583 1 + 82 . 1 1 48 48 LYS N N 15 124.90 0.20 . 1 . . . A 48 LYS N . 18583 1 + 83 . 1 1 50 50 LEU H H 1 8.74 0.05 . 1 . . . A 50 LEU H . 18583 1 + 84 . 1 1 50 50 LEU N N 15 126.43 0.20 . 1 . . . A 50 LEU N . 18583 1 + 85 . 1 1 51 51 GLU H H 1 8.49 0.05 . 1 . . . A 51 GLU H . 18583 1 + 86 . 1 1 51 51 GLU N N 15 123.28 0.20 . 1 . . . A 51 GLU N . 18583 1 + 87 . 1 1 52 52 ASP H H 1 8.20 0.05 . 1 . . . A 52 ASP H . 18583 1 + 88 . 1 1 52 52 ASP N N 15 120.85 0.20 . 1 . . . A 52 ASP N . 18583 1 + 89 . 1 1 54 54 ARG H H 1 7.46 0.05 . 1 . . . A 54 ARG H . 18583 1 + 90 . 1 1 54 54 ARG N N 15 119.64 0.20 . 1 . . . A 54 ARG N . 18583 1 + 91 . 1 1 55 55 THR H H 1 8.81 0.05 . 1 . . . A 55 THR H . 18583 1 + 92 . 1 1 55 55 THR N N 15 108.82 0.20 . 1 . . . A 55 THR N . 18583 1 + 93 . 1 1 56 56 LEU H H 1 8.14 0.05 . 1 . . . A 56 LEU H . 18583 1 + 94 . 1 1 56 56 LEU N N 15 118.15 0.20 . 1 . . . A 56 LEU N . 18583 1 + 95 . 1 1 57 57 SER H H 1 8.48 0.05 . 1 . . . A 57 SER H . 18583 1 + 96 . 1 1 57 57 SER N N 15 113.52 0.20 . 1 . . . A 57 SER N . 18583 1 + 97 . 1 1 58 58 ASP H H 1 7.97 0.05 . 1 . . . A 58 ASP H . 18583 1 + 98 . 1 1 58 58 ASP N N 15 124.93 0.20 . 1 . . . A 58 ASP N . 18583 1 + 99 . 1 1 59 59 TYR H H 1 7.21 0.05 . 1 . . . A 59 TYR H . 18583 1 + 100 . 1 1 59 59 TYR N N 15 115.77 0.20 . 1 . . . A 59 TYR N . 18583 1 + 101 . 1 1 60 60 ASN H H 1 8.16 0.05 . 1 . . . A 60 ASN H . 18583 1 + 102 . 1 1 60 60 ASN N N 15 115.93 0.20 . 1 . . . A 60 ASN N . 18583 1 + 103 . 1 1 61 61 ILE H H 1 7.34 0.05 . 1 . . . A 61 ILE H . 18583 1 + 104 . 1 1 61 61 ILE N N 15 119.34 0.20 . 1 . . . A 61 ILE N . 18583 1 + 105 . 1 1 62 62 GLN H H 1 7.65 0.05 . 1 . . . A 62 GLN H . 18583 1 + 106 . 1 1 62 62 GLN N N 15 125.07 0.20 . 1 . . . A 62 GLN N . 18583 1 + 107 . 1 1 63 63 LYS H H 1 8.49 0.05 . 1 . . . A 63 LYS H . 18583 1 + 108 . 1 1 63 63 LYS N N 15 120.68 0.20 . 1 . . . A 63 LYS N . 18583 1 + 109 . 1 1 64 64 GLU H H 1 9.32 0.05 . 1 . . . A 64 GLU H . 18583 1 + 110 . 1 1 64 64 GLU N N 15 115.09 0.20 . 1 . . . A 64 GLU N . 18583 1 + 111 . 1 1 65 65 SER H H 1 7.70 0.05 . 1 . . . A 65 SER H . 18583 1 + 112 . 1 1 65 65 SER N N 15 115.14 0.20 . 1 . . . A 65 SER N . 18583 1 + 113 . 1 1 66 66 THR H H 1 8.71 0.05 . 1 . . . A 66 THR H . 18583 1 + 114 . 1 1 66 66 THR N N 15 117.81 0.20 . 1 . . . A 66 THR N . 18583 1 + 115 . 1 1 67 67 LEU H H 1 9.34 0.05 . 1 . . . A 67 LEU H . 18583 1 + 116 . 1 1 67 67 LEU N N 15 127.88 0.20 . 1 . . . A 67 LEU N . 18583 1 + 117 . 1 1 68 68 HIS H H 1 8.94 0.05 . 1 . . . A 68 HIS H . 18583 1 + 118 . 1 1 68 68 HIS N N 15 118.71 0.20 . 1 . . . A 68 HIS N . 18583 1 + 119 . 1 1 69 69 LEU H H 1 8.70 0.05 . 1 . . . A 69 LEU H . 18583 1 + 120 . 1 1 69 69 LEU N N 15 124.84 0.20 . 1 . . . A 69 LEU N . 18583 1 + 121 . 1 1 70 70 VAL H H 1 8.70 0.05 . 1 . . . A 70 VAL H . 18583 1 + 122 . 1 1 70 70 VAL N N 15 128.09 0.20 . 1 . . . A 70 VAL N . 18583 1 + 123 . 1 1 71 71 LEU H H 1 8.16 0.05 . 1 . . . A 71 LEU H . 18583 1 + 124 . 1 1 71 71 LEU N N 15 123.45 0.20 . 1 . . . A 71 LEU N . 18583 1 + 125 . 1 1 72 72 ARG H H 1 8.53 0.05 . 1 . . . A 72 ARG H . 18583 1 + 126 . 1 1 72 72 ARG N N 15 122.16 0.20 . 1 . . . A 72 ARG N . 18583 1 + 127 . 1 1 73 73 LEU H H 1 8.53 0.05 . 1 . . . A 73 LEU H . 18583 1 + 128 . 1 1 73 73 LEU N N 15 123.81 0.20 . 1 . . . A 73 LEU N . 18583 1 + 129 . 1 1 74 74 ARG H H 1 8.47 0.05 . 1 . . . A 74 ARG H . 18583 1 + 130 . 1 1 74 74 ARG N N 15 122.07 0.20 . 1 . . . A 74 ARG N . 18583 1 + 131 . 1 1 76 76 GLY H H 1 7.99 0.05 . 1 . . . A 76 GLY H . 18583 1 + 132 . 1 1 76 76 GLY N N 15 115.39 0.20 . 1 . . . A 76 GLY N . 18583 1 + 133 . 2 2 4 4 GLN H H 1 8.260 0.05 . . . . . C 456 GLN H . 18583 1 + 134 . 2 2 4 4 GLN N N 15 123.150 0.3 . . . . . C 456 GLN N . 18583 1 + 135 . 2 2 5 5 LEU H H 1 8.110 0.05 . . . . . C 457 LEU H . 18583 1 + 136 . 2 2 5 5 LEU N N 15 120.050 0.3 . . . . . C 457 LEU N . 18583 1 + 137 . 2 2 6 6 ASN H H 1 8.090 0.05 . . . . . C 458 ASN H . 18583 1 + 138 . 2 2 6 6 ASN N N 15 115.900 0.3 . . . . . C 458 ASN N . 18583 1 + 139 . 2 2 7 7 ALA H H 1 7.840 0.05 . . . . . C 459 ALA H . 18583 1 + 140 . 2 2 7 7 ALA N N 15 122.890 0.3 . . . . . C 459 ALA N . 18583 1 + 141 . 2 2 8 8 MET H H 1 7.990 0.05 . . . . . C 460 MET H . 18583 1 + 142 . 2 2 8 8 MET N N 15 119.210 0.3 . . . . . C 460 MET N . 18583 1 + 143 . 2 2 9 9 ALA H H 1 8.360 0.05 . . . . . C 461 ALA H . 18583 1 + 144 . 2 2 9 9 ALA N N 15 121.420 0.3 . . . . . C 461 ALA N . 18583 1 + 145 . 2 2 10 10 HIS H H 1 8.200 0.05 . . . . . C 462 HIS H . 18583 1 + 146 . 2 2 10 10 HIS N N 15 117.430 0.3 . . . . . C 462 HIS N . 18583 1 + 147 . 2 2 11 11 GLN H H 1 7.840 0.05 . . . . . C 463 GLN H . 18583 1 + 148 . 2 2 11 11 GLN N N 15 118.610 0.3 . . . . . C 463 GLN N . 18583 1 + 149 . 2 2 12 12 ILE H H 1 7.850 0.05 . . . . . C 464 ILE H . 18583 1 + 150 . 2 2 12 12 ILE N N 15 118.710 0.3 . . . . . C 464 ILE N . 18583 1 + 151 . 2 2 13 13 GLN H H 1 8.600 0.05 . . . . . C 465 GLN H . 18583 1 + 152 . 2 2 13 13 GLN N N 15 120.500 0.3 . . . . . C 465 GLN N . 18583 1 + 153 . 2 2 14 14 GLU H H 1 7.450 0.05 . . . . . C 466 GLU H . 18583 1 + 154 . 2 2 14 14 GLU N N 15 115.72 0.3 . . . . . C 466 GLU N . 18583 1 + 155 . 2 2 15 15 MET H H 1 6.800 0.05 . . . . . C 467 MET H . 18583 1 + 156 . 2 2 15 15 MET N N 15 115.080 0.3 . . . . . C 467 MET N . 18583 1 + 157 . 2 2 16 16 PHE H H 1 7.870 0.05 . . . . . C 468 PHE H . 18583 1 + 158 . 2 2 16 16 PHE N N 15 113.750 0.3 . . . . . C 468 PHE N . 18583 1 + 159 . 2 2 18 18 GLN H H 1 9.500 0.05 . . . . . C 470 GLN H . 18583 1 + 160 . 2 2 18 18 GLN N N 15 116.900 0.3 . . . . . C 470 GLN N . 18583 1 + 161 . 2 2 19 19 VAL H H 1 7.7660 0.05 . . . . . C 471 VAL H . 18583 1 + 162 . 2 2 19 19 VAL N N 15 124.44 0.3 . . . . . C 471 VAL N . 18583 1 + 163 . 2 2 21 21 TYR H H 1 8.830 0.05 . . . . . C 473 TYR H . 18583 1 + 164 . 2 2 21 21 TYR N N 15 126.320 0.3 . . . . . C 473 TYR N . 18583 1 + 165 . 2 2 22 22 HIS H H 1 8.680 0.05 . . . . . C 474 HIS H . 18583 1 + 166 . 2 2 22 22 HIS N N 15 113.220 0.3 . . . . . C 474 HIS N . 18583 1 + 167 . 2 2 23 23 LEU H H 1 6.600 0.05 . . . . . C 475 LEU H . 18583 1 + 168 . 2 2 23 23 LEU N N 15 119.450 0.3 . . . . . C 475 LEU N . 18583 1 + 169 . 2 2 24 24 VAL H H 1 7.180 0.05 . . . . . C 476 VAL H . 18583 1 + 170 . 2 2 24 24 VAL N N 15 120.890 0.3 . . . . . C 476 VAL N . 18583 1 + 171 . 2 2 25 25 LEU H H 1 8.100 0.05 . . . . . C 477 LEU H . 18583 1 + 172 . 2 2 25 25 LEU N N 15 118.710 0.3 . . . . . C 477 LEU N . 18583 1 + 173 . 2 2 26 26 GLN H H 1 7.550 0.05 . . . . . C 478 GLN H . 18583 1 + 174 . 2 2 26 26 GLN N N 15 115.520 0.3 . . . . . C 478 GLN N . 18583 1 + 175 . 2 2 27 27 ASP H H 1 7.390 0.05 . . . . . C 479 ASP H . 18583 1 + 176 . 2 2 27 27 ASP N N 15 119.110 0.3 . . . . . C 479 ASP N . 18583 1 + 177 . 2 2 28 28 LEU H H 1 8.400 0.05 . . . . . C 480 LEU H . 18583 1 + 178 . 2 2 28 28 LEU N N 15 118.990 0.3 . . . . . C 480 LEU N . 18583 1 + 179 . 2 2 29 29 GLN H H 1 8.030 0.05 . . . . . C 481 GLN H . 18583 1 + 180 . 2 2 29 29 GLN N N 15 116.850 0.3 . . . . . C 481 GLN N . 18583 1 + 181 . 2 2 30 30 LEU H H 1 7.230 0.05 . . . . . C 482 LEU H . 18583 1 + 182 . 2 2 30 30 LEU N N 15 117.030 0.3 . . . . . C 482 LEU N . 18583 1 + 183 . 2 2 31 31 THR H H 1 8.870 0.05 . . . . . C 483 THR H . 18583 1 + 184 . 2 2 31 31 THR N N 15 110.740 0.3 . . . . . C 483 THR N . 18583 1 + 185 . 2 2 32 32 ARG H H 1 9.030 0.05 . . . . . C 484 ARG H . 18583 1 + 186 . 2 2 32 32 ARG N N 15 117.784 0.3 . . . . . C 484 ARG N . 18583 1 + 187 . 2 2 33 33 SER H H 1 7.971 0.05 . . . . . C 485 SER H . 18583 1 + 188 . 2 2 33 33 SER N N 15 110.880 0.3 . . . . . C 485 SER N . 18583 1 + 189 . 2 2 34 34 VAL H H 1 9.060 0.05 . . . . . C 486 VAL H . 18583 1 + 190 . 2 2 34 34 VAL N N 15 129.980 0.3 . . . . . C 486 VAL N . 18583 1 + 191 . 2 2 35 35 GLU H H 1 9.270 0.05 . . . . . C 487 GLU H . 18583 1 + 192 . 2 2 35 35 GLU N N 15 123.360 0.3 . . . . . C 487 GLU N . 18583 1 + 193 . 2 2 36 36 ILE H H 1 7.980 0.05 . . . . . C 488 ILE H . 18583 1 + 194 . 2 2 36 36 ILE N N 15 119.880 0.3 . . . . . C 488 ILE N . 18583 1 + 195 . 2 2 37 37 THR H H 1 8.250 0.05 . . . . . C 489 THR H . 18583 1 + 196 . 2 2 37 37 THR N N 15 118.020 0.3 . . . . . C 489 THR N . 18583 1 + 197 . 2 2 38 38 THR H H 1 8.350 0.05 . . . . . C 490 THR H . 18583 1 + 198 . 2 2 38 38 THR N N 15 117.400 0.3 . . . . . C 490 THR N . 18583 1 + 199 . 2 2 39 39 ASP H H 1 7.490 0.05 . . . . . C 491 ASP H . 18583 1 + 200 . 2 2 39 39 ASP N N 15 122.260 0.3 . . . . . C 491 ASP N . 18583 1 + 201 . 2 2 40 40 ASN H H 1 8.490 0.05 . . . . . C 492 ASN H . 18583 1 + 202 . 2 2 40 40 ASN N N 15 116.340 0.3 . . . . . C 492 ASN N . 18583 1 + 203 . 2 2 41 41 ILE H H 1 8.000 0.05 . . . . . C 493 ILE H . 18583 1 + 204 . 2 2 41 41 ILE N N 15 121.110 0.3 . . . . . C 493 ILE N . 18583 1 + 205 . 2 2 42 42 LEU H H 1 8.410 0.05 . . . . . C 494 LEU H . 18583 1 + 206 . 2 2 42 42 LEU N N 15 121.930 0.3 . . . . . C 494 LEU N . 18583 1 + 207 . 2 2 43 43 GLU H H 1 8.370 0.05 . . . . . C 495 GLU H . 18583 1 + 208 . 2 2 43 43 GLU N N 15 114.530 0.3 . . . . . C 495 GLU N . 18583 1 + 209 . 2 2 44 44 GLY H H 1 7.630 0.05 . . . . . C 496 GLY H . 18583 1 + 210 . 2 2 44 44 GLY N N 15 107.200 0.3 . . . . . C 496 GLY N . 18583 1 + 211 . 2 2 45 45 ARG H H 1 8.300 0.05 . . . . . C 497 ARG H . 18583 1 + 212 . 2 2 45 45 ARG N N 15 116.830 0.3 . . . . . C 497 ARG N . 18583 1 + 213 . 2 2 46 46 ILE H H 1 7.130 0.05 . . . . . C 498 ILE H . 18583 1 + 214 . 2 2 46 46 ILE N N 15 117.930 0.3 . . . . . C 498 ILE N . 18583 1 + 215 . 2 2 47 47 GLN H H 1 8.340 0.05 . . . . . C 499 GLN H . 18583 1 + 216 . 2 2 47 47 GLN N N 15 125.410 0.3 . . . . . C 499 GLN N . 18583 1 + 217 . 2 2 48 48 VAL H H 1 8.180 0.05 . . . . . C 500 VAL H . 18583 1 + 218 . 2 2 48 48 VAL N N 15 122.810 0.3 . . . . . C 500 VAL N . 18583 1 + 219 . 2 2 50 50 PHE H H 1 8.115 0.05 . . . . . C 502 PHE H . 18583 1 + 220 . 2 2 50 50 PHE N N 15 121.190 0.3 . . . . . C 502 PHE N . 18583 1 + 221 . 2 2 52 52 THR H H 1 7.790 0.05 . . . . . C 504 THR H . 18583 1 + 222 . 2 2 52 52 THR N N 15 119.528 0.3 . . . . . C 504 THR N . 18583 1 + + stop_ + +save_ + diff --git a/example/input.toml b/example/input.toml index 454703d..da576bd 100644 --- a/example/input.toml +++ b/example/input.toml @@ -1,25 +1,18 @@ #------------------------------------------------------------------------------------------------ [general] -sequence = "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG" +sequence = "TLTGKTITLEVEPSDTIENVKAKIQDKEGQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG" secondary_structure = "" fractionally_deuterated = true #------------------------------------------------------------------------------------------------ [BMRB] -# BMRB tables as a text file in NMR Star format -# bmrb_table_fname = "1ubq-bmrb-tables.txt" -bmrb_table_fname = "" -# Which should be the first residue number of your sequence. -sequence_start = 1 -# column numbers -resnum_column = 1 -atom_column = 3 -chemical_shift_column = 4 +# BMRB tables as a text file in NMR-STAR v3.1+ format +bmrb_table_fname = "bmr18583_3.str" +target_entity = 1 #------------------------------------------------------------------------------------------------ [distance] distance_fname = "1ubq-cc-dist.txt" -# distance_fname = "" distance_cutoff = 3.9 #------------------------------------------------------------------------------------------------ @@ -40,10 +33,10 @@ rev_14n = ["I"] #------------------------------------------------------------------------------------------------ [preset_experiments] selected = [ - "N-H", - "N-(Calpha)-Cx (residues i, i+1 & i-1)", - "N-(Co)-Cx", - "C-C DQ-SQ Correlation", + "N-H", + "N-(Calpha)-Cx (residues i, i+1 & i-1)", + "N-(Co)-Cx", + "C-C DQ-SQ Correlation", ] #------------------------------------------------------------------------------------------------ diff --git a/requirements.txt b/requirements.txt index a8afa4d..be21912 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,4 @@ numpy==1.22.3 pandas==1.4.2 toml==0.10.2 +pynmrstar==3.1.0 diff --git a/src/fandas/cli.py b/src/fandas/cli.py index 9d97e85..4b4ff1e 100644 --- a/src/fandas/cli.py +++ b/src/fandas/cli.py @@ -2,6 +2,7 @@ import logging import sys +# from fandas.modules.bmrb import BMRB from fandas.modules.chemical_shift import ChemShift from fandas.modules.experiment import Experiment from fandas.modules.input import InputFile @@ -66,7 +67,12 @@ def main( log.info(f" Welcome to FANDAS {VERSION}") log.info("########################################") - inp = InputFile(input_file) + try: + inp = InputFile(input_file) + except Exception as e: + log.error("Error loading input file") + log.error(e) + sys.exit() # Read input sequence # ==========================================================# sequence = inp.data["general"]["sequence"] @@ -89,27 +95,13 @@ def main( secondary_structure = secondary_structure[: len(sequence)] # Assign chemical shifts #========================================================# - log.info("Assigning average shifts") - - chem_shifts = ChemShift(sequence, secondary_structure) - chem_shifts.assign() - - # Replace the average shifts with provided shifts in the form of BMRB table ======# - bmrb_table_fname = inp.data["BMRB"]["bmrb_table_fname"] - if bmrb_table_fname: - - resnum_col = inp.data["BMRB"]["resnum_column"] - atom_col = inp.data["BMRB"]["atom_column"] - shift_col = inp.data["BMRB"]["chemical_shift_column"] - bt_seq_start = inp.data["BMRB"]["sequence_start"] - - log.info( - "Replacing the average shifts with provided " - "shifts in the form of BMRB table" - ) - chem_shifts.replace_with_bmrb( - bmrb_table_fname, resnum_col, atom_col, shift_col, bt_seq_start - ) + log.info("Assigning chemical shifts") + + # Read BMRB table + bmrb_table = inp.data["BMRB"]["bmrb_table_fname"] + bmrb_entity_id = inp.data["BMRB"]["target_entity"] + + chem_shifts = ChemShift(sequence, secondary_structure, bmrb_table, bmrb_entity_id) # Incorporate forward, reverse & glycerol labeling schemes #=====================# labeling_params = inp.data["labeling"] diff --git a/src/fandas/modules/bmrb.py b/src/fandas/modules/bmrb.py new file mode 100644 index 0000000..ec7b273 --- /dev/null +++ b/src/fandas/modules/bmrb.py @@ -0,0 +1,102 @@ +import logging +import sys + +import pynmrstar +from Bio import Align +from Bio.Align import substitution_matrices +from Bio.Seq import Seq +from pynmrstar.exceptions import ParsingError + +from fandas.modules.chemical import THREE_TO_ONE +from fandas.modules.residue import Residue + +log = logging.getLogger("fandaslog") + + +class BMRB: + def __init__(self, table_fname, entity_id): + self.table_fname = str(table_fname) + self.target_entity_id = entity_id + self.entry, self.residues, self.sequence = self._read() + self._assign() + + def _assign(self): + """Assign the BMRB shifts to the residues.""" + for _loop in self.entry.get_loops_by_category("_Atom_chem_shift"): + for element in _loop.get_tag( + ["Entity_assembly_ID", "Seq_ID", "Comp_ID", "Atom_ID", "Val"] + ): + entity_id, resnum, resname, atom, value = element + entity_id = int(entity_id) + if entity_id != self.target_entity_id: + continue + resnum = int(resnum) + value = float(value) + resname = THREE_TO_ONE[resname] + # + if resnum not in self.residues: + self.residues[resnum] = Residue(resnum, resname, None, {}) + self.residues[resnum].shifts[atom] = value + + def align_to(self, reference_sequence): + """Align the BRMB table to the reference sequence.""" + target_seq = self.sequence + reference_seq = Seq(reference_sequence) + aligner = Align.PairwiseAligner(open_gap_score=-10) + aligner.substitution_matrix = substitution_matrices.load("BLOSUM62") + alns = aligner.align(reference_seq, target_seq) + top_aln = alns[0] + identity = ( + str(top_aln).count("|") / float(min(len(reference_seq), len(target_seq))) + ) * 100 + log.info(f"Identity: {identity:.2f}%") + for line in str(top_aln).split(): + log.info(line) + if identity <= 70: + log.warning("") + log.warning("!!! Identity is low !!!") + log.warning("Are you sure this is the correct entity?") + log.warning("!!! Identity is low !!!") + log.warning("") + + aligned_ref_segment, aligned_model_segment = top_aln.aligned + align_dict = {} + for ref_segment, model_segment in zip( + aligned_ref_segment, aligned_model_segment + ): + + start_ref_segment, end_ref_segment = ref_segment + start_entity_segment, end_entity_segment = model_segment + + for _ref_pos, _entity_pos in zip( + range(start_ref_segment, end_ref_segment), + range(start_entity_segment, end_entity_segment), + ): + align_dict[_ref_pos + 1] = _entity_pos + 1 + return align_dict + + def _read(self): + """Use pyNMRStar to read the BMRB table.""" + try: + entry = pynmrstar.Entry.from_file(self.table_fname) + except ParsingError as e: + log.error(e) + sys.exit() + + residue_dict = {} + seq = "" + for _loop in entry.get_loops_by_category("_Entity_poly_seq"): + for i, element in enumerate( + _loop.get_tag(["Mon_ID", "Entity_ID"]), start=1 + ): + resname, entity_id = element + resname_one_letter = THREE_TO_ONE[resname] + if int(entity_id) == self.target_entity_id: + try: + seq += resname_one_letter + except KeyError: + seq += "X" + + residue_dict[i] = Residue(i, resname_one_letter, None, {}) + + return entry, residue_dict, seq diff --git a/src/fandas/modules/chemical.py b/src/fandas/modules/chemical.py index 3e15689..dcc8ac1 100644 --- a/src/fandas/modules/chemical.py +++ b/src/fandas/modules/chemical.py @@ -3,7 +3,6 @@ import toml - STANDARD_DATA = Path(Path(__file__).parents[1], "data/standard.csv") @@ -553,3 +552,49 @@ "Y": ["HA"], "V": ["HA", "HB"], } + +THREE_TO_ONE = { + "CYS": "C", + "ASP": "D", + "SER": "S", + "GLN": "Q", + "LYS": "K", + "ILE": "I", + "PRO": "P", + "THR": "T", + "PHE": "F", + "ASN": "N", + "GLY": "G", + "HIS": "H", + "LEU": "L", + "ARG": "R", + "TRP": "W", + "ALA": "A", + "VAL": "V", + "GLU": "E", + "TYR": "Y", + "MET": "M", +} + +ONE_TO_THREE = { + "C": "CYS", + "D": "ASP", + "S": "SER", + "Q": "GLN", + "K": "LYS", + "I": "ILE", + "P": "PRO", + "T": "THR", + "F": "PHE", + "N": "ASN", + "G": "GLY", + "H": "HIS", + "L": "LEU", + "R": "ARG", + "W": "TRP", + "A": "ALA", + "V": "VAL", + "E": "GLU", + "Y": "TYR", + "M": "MET", +} diff --git a/src/fandas/modules/chemical_shift.py b/src/fandas/modules/chemical_shift.py index cc38ede..efadea9 100644 --- a/src/fandas/modules/chemical_shift.py +++ b/src/fandas/modules/chemical_shift.py @@ -1,7 +1,10 @@ import logging +import sys from functools import partial import pandas as pd + +from fandas.modules.bmrb import BMRB from fandas.modules.chemical import ( AA_REF, C_ATOMS, @@ -13,16 +16,17 @@ STANDARD_DATA, ) from fandas.modules.residue import Residue -from fandas.modules.utils import load_bmrbm log = logging.getLogger("fandaslog") class ChemShift: - def __init__(self, sequence, secondary_structure): + def __init__(self, sequence, secondary_structure, bmrb_table, bmrb_entity_id): self.residues = {} self.sequence = sequence self.secondary_structure = secondary_structure + self.bmrb_table = bmrb_table + self.bmrb_entity_id = bmrb_entity_id self.assign() def assign(self, data=STANDARD_DATA): @@ -51,39 +55,40 @@ def assign(self, data=STANDARD_DATA): self.residues[resnum] = Residue(resnum, resname, ss, atom_shift_dic) - def replace_with_bmrb( - self, table_fname, resnum_col, atom_col, shift_col, seq_offset - ): - """Use a BMRB table to replace the default shift values.""" - bmrb_data = load_bmrbm(table_fname, resnum_col, atom_col, shift_col) - - for bmrb_resnum in bmrb_data: - seq_resnum = (bmrb_resnum - seq_offset) + 1 + if self.bmrb_table: try: - seq_resname = self.residues[seq_resnum].resname - except KeyError: - log.warning( - f"Could not find residue {bmrb_resnum} in sequence. Skipping." - ) - continue - - for bmrb_atom in bmrb_data[bmrb_resnum]: - new_shift = bmrb_data[bmrb_resnum][bmrb_atom] - - # replace - try: - old_shift = self.residues[seq_resnum].shifts[bmrb_atom] + self.use_bmrb() + except Exception as e: + log.exception(e) + sys.exit() + + def use_bmrb(self): + """Use the BMRB table.""" + entry = BMRB(self.bmrb_table, self.bmrb_entity_id) + log.info(f"Aligning input sequence with BMRB entity {self.bmrb_entity_id}") + alignment_dict = entry.align_to(self.sequence) + log.info("Updating shifts based on BMRB table") + self._update_shifts(entry, alignment_dict) + + def _update_shifts(self, bmrb_entry, alignment_dict): + """Update the chemical shifts based on the BMRB table.""" + for element in enumerate(self.residues.items()): + position, _ = element + _, standard_residue = list(self.residues.items())[position] + matching_pos = alignment_dict[position + 1] + _, bmrb_residue = list(bmrb_entry.residues.items())[matching_pos - 1] + + assert bmrb_residue.resname == standard_residue.resname + + for atom in standard_residue.shifts: + if atom in bmrb_residue.shifts: log.info( - f"# (bmrb.{bmrb_resnum}) {bmrb_resnum}\t{seq_resname}" - f"\t{bmrb_atom}\t{old_shift}\t>> {new_shift}" - ) - - self.residues[seq_resnum].shifts[bmrb_atom] = new_shift - except KeyError: - log.warning( - f"# (bmrb.{bmrb_resnum}) {bmrb_resnum}\t atom: " - f"{bmrb_atom} not found in standard table, skipping..." + f"# (bmrb.{bmrb_residue.resnum}) {bmrb_residue.resnum}\t" + f"{bmrb_residue.resname}\t{atom}\t" + f"{standard_residue.shifts[atom]}\t" + f">> {bmrb_residue.shifts[atom]}" ) + standard_residue.shifts[atom] = bmrb_residue.shifts[atom] def label(self, params): """Apply a labeling scheme.""" diff --git a/src/fandas/modules/input.py b/src/fandas/modules/input.py index 3837c58..bc26560 100644 --- a/src/fandas/modules/input.py +++ b/src/fandas/modules/input.py @@ -1,4 +1,3 @@ -from os import stat import toml @@ -7,12 +6,23 @@ class InputFile: def __init__(self, input_f): self.data = self._load(input_f) + self._validate() - @staticmethod - def _validate(data): + def _validate(self): """Validate if the fields are correct.""" # FIXME: Implement! - pass + + # validate BMRB fields + if "BMRB" not in self.data: + # these can be empty + self.data["BMRB"] = {} + self.data["BMRB"]["bmrb_table_fname"] = None + self.data["BMRB"]["target_entity"] = None + else: + if "bmrb_table_fname" not in self.data["BMRB"]: + raise ValueError("Missing `bmrb_table_fname` parameter in BMRB section") + if "target_entity" not in self.data["BMRB"]: + raise ValueError("Missing `target_entity` parameter in BMRB section") @staticmethod def _load(input_f): diff --git a/src/fandas/modules/utils.py b/src/fandas/modules/utils.py index ab5a967..8575ed2 100644 --- a/src/fandas/modules/utils.py +++ b/src/fandas/modules/utils.py @@ -1,29 +1 @@ -import logging - -log = logging.getLogger("fandaslog") - - -def load_bmrbm(table_fname, resname_col, atom_col, shift_col): - """Load a BMRBM table and return a dictionary.""" - bmrb_dic = {} - with open(table_fname, "r") as bmrb_file: - for line in bmrb_file.readlines(): - - # Split so that the whitespaces don't matter - c_shift = line.split() - - if not c_shift: - # line is empty - continue - - # bmrb_columns starts with index 1 so here we need to -1 all positions - bmrb_resnum = int(c_shift[resname_col - 1]) - bmrb_atom = c_shift[atom_col - 1] - bmrb_shift = float(c_shift[shift_col - 1]) - - if bmrb_resnum not in bmrb_dic: - bmrb_dic[bmrb_resnum] = {} - - bmrb_dic[bmrb_resnum][bmrb_atom] = bmrb_shift - - return bmrb_dic +"""Nothing here!.""" diff --git a/tests/__init__.py b/tests/__init__.py index d0e58e7..fadca0a 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -2,6 +2,6 @@ from pathlib import Path TEST_DATA_PATH = Path(Path(__file__).resolve().parents[0], "data") -TEST_BMRB_TABLE = Path(TEST_DATA_PATH, "test_bmrm_table.csv") +TEST_BMRB_TABLE = Path(TEST_DATA_PATH, "test_bmrm.str") TEST_INPUT_FILE = Path(TEST_DATA_PATH, "test_input.toml") TEST_DISTANCE_FILE = Path(TEST_DATA_PATH, "test_distance.txt") diff --git a/tests/data/test_bmrm.str b/tests/data/test_bmrm.str new file mode 100644 index 0000000..a2acf18 --- /dev/null +++ b/tests/data/test_bmrm.str @@ -0,0 +1,1945 @@ +data_18583 + +####################### +# Entry information # +####################### + +save_entry_information + _Entry.Sf_category entry_information + _Entry.Sf_framecode entry_information + _Entry.ID 18583 + _Entry.Title +; +Solution structure of the gp78CUE/K48-Ub2 complex +; + _Entry.Type macromolecule + _Entry.Version_type original + _Entry.Submission_date 2012-07-09 + _Entry.Accession_date 2012-07-09 + _Entry.Last_release_date . + _Entry.Original_release_date . + _Entry.Origination author + _Entry.NMR_STAR_version 3.1.1.61 + _Entry.Original_NMR_STAR_version 3.1 + _Entry.Experimental_method NMR + _Entry.Experimental_method_subtype SOLUTION + _Entry.Details 'Amide shifts of gp78CUE and distal Ubiquitin in the gp78CUE/K48-Ub2 complex' + _Entry.BMRB_internal_directory_name . + + loop_ + _Entry_author.Ordinal + _Entry_author.Given_name + _Entry_author.Family_name + _Entry_author.First_initial + _Entry_author.Middle_initials + _Entry_author.Family_title + _Entry_author.Entry_ID + + 1 Shan Liu . . . 18583 + 2 Yinghua Chen . . . 18583 + 3 Tao Huang . . . 18583 + 4 Sergey Tarasov . G. . 18583 + 5 Aaren King . . . 18583 + 6 Jess Li . . . 18583 + 7 Allan Weissman . M. . 18583 + 8 Robert Byrd . A. . 18583 + 9 Ranabir Das . . . 18583 + + stop_ + + loop_ + _SG_project.SG_project_ID + _SG_project.Project_name + _SG_project.Full_name_of_center + _SG_project.Initial_of_center + _SG_project.Entry_ID + + 1 'not applicable' 'not applicable' . 18583 + + stop_ + + loop_ + _Struct_keywords.Keywords + _Struct_keywords.Text + _Struct_keywords.Entry_ID + + CUE . 18583 + gp78 . 18583 + NMR . 18583 + Protein . 18583 + + stop_ + + loop_ + _Data_set.Type + _Data_set.Count + _Data_set.Entry_ID + + assigned_chemical_shifts 1 18583 + + stop_ + + loop_ + _Datum.Type + _Datum.Count + _Datum.Entry_ID + + '15N chemical shifts' 111 18583 + '1H chemical shifts' 111 18583 + + stop_ + + loop_ + _Release.Release_number + _Release.Format_type + _Release.Format_version + _Release.Date + _Release.Submission_date + _Release.Type + _Release.Author + _Release.Detail + _Release.Entry_ID + + 2 . . 2013-02-19 2012-07-09 update BMRB 'update entry citation' 18583 + 1 . . 2012-11-19 2012-07-09 original author 'original release' 18583 + + stop_ + + loop_ + _Related_entries.Database_name + _Related_entries.Database_accession_code + _Related_entries.Relationship + _Related_entries.Entry_ID + + BMRB 18581 'gp78 CUE domain' 18583 + BMRB 18582 'gp78CUE bound to ubiquitin' 18583 + BMRB 18584 'gp78CUE/K48-Ub2 complex' 18583 + PDB 2LVP 'BMRB Entry Tracking System' 18583 + + stop_ + +save_ + + +############### +# Citations # +############### + +save_entry_citation + _Citation.Sf_category citations + _Citation.Sf_framecode entry_citation + _Citation.Entry_ID 18583 + _Citation.ID 1 + _Citation.Class 'entry citation' + _Citation.CAS_abstract_code . + _Citation.MEDLINE_UI_code . + _Citation.DOI . + _Citation.PubMed_ID 23123110 + _Citation.Full_citation . + _Citation.Title 'Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains.' + _Citation.Status published + _Citation.Type journal + _Citation.Journal_abbrev Structure + _Citation.Journal_name_full 'Structure (London, England : 1993)' + _Citation.Journal_volume 20 + _Citation.Journal_issue 12 + _Citation.Journal_ASTM . + _Citation.Journal_ISSN . + _Citation.Journal_CSD . + _Citation.Book_title . + _Citation.Book_chapter_title . + _Citation.Book_volume . + _Citation.Book_series . + _Citation.Book_publisher . + _Citation.Book_publisher_city . + _Citation.Book_ISBN . + _Citation.Conference_title . + _Citation.Conference_site . + _Citation.Conference_state_province . + _Citation.Conference_country . + _Citation.Conference_start_date . + _Citation.Conference_end_date . + _Citation.Conference_abstract_number . + _Citation.Thesis_institution . + _Citation.Thesis_institution_city . + _Citation.Thesis_institution_country . + _Citation.WWW_URL . + _Citation.Page_first 2138 + _Citation.Page_last 2150 + _Citation.Year 2012 + _Citation.Details . + + loop_ + _Citation_author.Ordinal + _Citation_author.Given_name + _Citation_author.Family_name + _Citation_author.First_initial + _Citation_author.Middle_initials + _Citation_author.Family_title + _Citation_author.Entry_ID + _Citation_author.Citation_ID + + 1 Shan Liu . . . 18583 1 + 2 Yinghua Chen . . . 18583 1 + 3 Jess Li . . . 18583 1 + 4 Tao Huang . . . 18583 1 + 5 Sergey Tarasov . . . 18583 1 + 6 Aaren King . . . 18583 1 + 7 Allan Weissman . M. . 18583 1 + 8 'R. Andrew' Byrd . . . 18583 1 + 9 Ranabir Das . . . 18583 1 + + stop_ + +save_ + + +############################################# +# Molecular system (assembly) description # +############################################# + +save_assembly + _Assembly.Sf_category assembly + _Assembly.Sf_framecode assembly + _Assembly.Entry_ID 18583 + _Assembly.ID 1 + _Assembly.Name 'gp78CUE/K48-Ub2 complex' + _Assembly.BMRB_code . + _Assembly.Number_of_components 3 + _Assembly.Organic_ligands . + _Assembly.Metal_ions . + _Assembly.Non_standard_bonds . + _Assembly.Ambiguous_conformational_states . + _Assembly.Ambiguous_chem_comp_sites . + _Assembly.Molecules_in_chemical_exchange . + _Assembly.Paramagnetic no + _Assembly.Thiol_state . + _Assembly.Molecular_mass . + _Assembly.Enzyme_commission_number . + _Assembly.Details . + _Assembly.DB_query_date . + _Assembly.DB_query_revised_last_date . + + loop_ + _Entity_assembly.ID + _Entity_assembly.Entity_assembly_name + _Entity_assembly.Entity_ID + _Entity_assembly.Entity_label + _Entity_assembly.Asym_ID + _Entity_assembly.PDB_chain_ID + _Entity_assembly.Experimental_data_reported + _Entity_assembly.Physical_state + _Entity_assembly.Conformational_isomer + _Entity_assembly.Chemical_exchange_state + _Entity_assembly.Magnetic_equivalence_group_code + _Entity_assembly.Role + _Entity_assembly.Details + _Entity_assembly.Entry_ID + _Entity_assembly.Assembly_ID + + 1 ubiquitin_1 1 $entity_1 A . yes native no no . . . 18583 1 + 2 gp78CUE 2 $entity_2 C . yes native no no . . . 18583 1 + + stop_ + +save_ + + + #################################### + # Biological polymers and ligands # + #################################### + +save_entity_1 + _Entity.Sf_category entity + _Entity.Sf_framecode entity_1 + _Entity.Entry_ID 18583 + _Entity.ID 1 + _Entity.BMRB_code . + _Entity.Name ubiquitin + _Entity.Type polymer + _Entity.Polymer_common_type . + _Entity.Polymer_type polypeptide(L) + _Entity.Polymer_type_details . + _Entity.Polymer_strand_ID A,B + _Entity.Polymer_seq_one_letter_code_can . + _Entity.Polymer_seq_one_letter_code +; +MQIFVKTLTGKTITLEVEPS +DTIENVKAKIQDKEGIPPDQ +QRLIFAGKQLEDGRTLSDYN +IQKESTLHLVLRLRGG +; + _Entity.Target_identifier . + _Entity.Polymer_author_defined_seq . + _Entity.Polymer_author_seq_details . + _Entity.Ambiguous_conformational_states no + _Entity.Ambiguous_chem_comp_sites no + _Entity.Nstd_monomer no + _Entity.Nstd_chirality no + _Entity.Nstd_linkage no + _Entity.Nonpolymer_comp_ID . + _Entity.Nonpolymer_comp_label . + _Entity.Number_of_monomers 76 + _Entity.Number_of_nonpolymer_components . + _Entity.Paramagnetic no + _Entity.Thiol_state 'not present' + _Entity.Src_method man + _Entity.Parent_entity_ID . + _Entity.Fragment . + _Entity.Mutation . + _Entity.EC_number . + _Entity.Calc_isoelectric_point . + _Entity.Formula_weight 8576.914 + _Entity.Formula_weight_exptl . + _Entity.Formula_weight_exptl_meth . + _Entity.Details . + _Entity.DB_query_date . + _Entity.DB_query_revised_last_date 2015-11-25 + + loop_ + _Entity_db_link.Ordinal + _Entity_db_link.Author_supplied + _Entity_db_link.Database_code + _Entity_db_link.Accession_code + _Entity_db_link.Entry_mol_code + _Entity_db_link.Entry_mol_name + _Entity_db_link.Entry_experimental_method + _Entity_db_link.Entry_structure_resolution + _Entity_db_link.Entry_relation_type + _Entity_db_link.Entry_details + _Entity_db_link.Chimera_segment_ID + _Entity_db_link.Seq_query_to_submitted_percent + _Entity_db_link.Seq_subject_length + _Entity_db_link.Seq_identity + _Entity_db_link.Seq_positive + _Entity_db_link.Seq_homology_expectation_val + _Entity_db_link.Seq_align_begin + _Entity_db_link.Seq_align_end + _Entity_db_link.Seq_difference_details + _Entity_db_link.Seq_alignment_details + _Entity_db_link.Entry_ID + _Entity_db_link.Entity_ID + + 1 no BMRB 11505 . entity . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 2 no BMRB 11547 . ubiquitin . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 3 no BMRB 15047 . denatured_ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 4 no BMRB 15410 . Ubi . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 5 no BMRB 15689 . UBB . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 6 no BMRB 15907 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 7 no BMRB 16228 . ubiquitin . . . . . 100.00 76 97.37 98.68 1.73e-44 . . . . 18583 1 + 8 no BMRB 16582 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 9 no BMRB 16626 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 10 no BMRB 16895 . UBB+1 . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 11 no BMRB 17181 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 12 no BMRB 17439 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 13 no BMRB 17769 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 14 no BMRB 17919 . entity . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 15 no BMRB 18582 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 16 no BMRB 18584 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 17 no BMRB 18610 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 18 no BMRB 18611 . Ubiquitin_A_state . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 19 no BMRB 18737 . UBIQUITIN . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 20 no BMRB 19406 . entity . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 21 no BMRB 19412 . entity . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 22 no BMRB 25070 . Ubiquitin . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 23 no BMRB 25123 . Ubiquitin . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 24 no BMRB 25601 . entity_1 . . . . . 100.00 76 97.37 97.37 5.31e-44 . . . . 18583 1 + 25 no BMRB 26604 . Ubiquitin_(microcrystalline) . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 26 no BMRB 4245 . ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 27 no BMRB 4375 . Ubiquitin . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 28 no PDB 1AAR . "Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 29 no PDB 1CMX . "Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 30 no PDB 1D3Z . "Ubiquitin Nmr Structure" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 31 no PDB 1F9J . "Structure Of A New Crystal Form Of Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 32 no PDB 1FXT . "Structure Of A Conjugating Enzyme-Ubiquitin Thiolester Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 33 no PDB 1G6J . "Structure Of Recombinant Human Ubiquitin In Aot Reverse Micelles" . . . . . 98.68 76 100.00 100.00 7.58e-45 . . . . 18583 1 + 34 no PDB 1GJZ . "Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin" . . . . . 67.11 53 100.00 100.00 3.14e-26 . . . . 18583 1 + 35 no PDB 1NBF . "Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme In Isolation And In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 36 no PDB 1OGW . "Synthetic Ubiquitin With Fluoro-Leu At 50 And 67" . . . . . 100.00 76 97.37 97.37 2.65e-44 . . . . 18583 1 + 37 no PDB 1P3Q . "Mechanism Of Ubiquitin Recognition By The Cue Domain Of Vps9" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 38 no PDB 1Q5W . "Ubiquitin Recognition By Npl4 Zinc-Fingers" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 39 no PDB 1S1Q . "Tsg101(Uev) Domain In Complex With Ubiquitin" . . . . . 98.68 76 100.00 100.00 7.58e-45 . . . . 18583 1 + 40 no PDB 1TBE . "Structure Of Tetraubiquitin Shows How Multiubiquitin Chains Can Be Formed" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 41 no PDB 1UBI . "Synthetic Structural And Biological Studies Of The Ubiquitin System. Part 1" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 42 no PDB 1UBQ . "Structure Of Ubiquitin Refined At 1.8 Angstroms Resolution" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 43 no PDB 1UZX . "A Complex Of The Vps23 Uev With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 44 no PDB 1V80 . "Solution Structures Of Ubiquitin At 30 Bar And 3 Kbar" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 45 no PDB 1V81 . "Solution Structures Of Ubiquitin At 30 Bar And 3 Kbar" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 46 no PDB 1VX7 . "Cryo-em Structure Of The Plasmodium Falciparum 80s Ribosome Bound To The Anti-protozoan Drug Emetine, Large Subunit (protein On" . . . . . 100.00 128 98.68 100.00 1.38e-45 . . . . 18583 1 + 47 no PDB 1WR6 . "Crystal Structure Of Gga3 Gat Domain In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 48 no PDB 1WRD . "Crystal Structure Of Tom1 Gat Domain In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 49 no PDB 1XD3 . "Crystal Structure Of Uchl3-Ubvme Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 50 no PDB 1XQQ . "Simultaneous Determination Of Protein Structure And Dynamics" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 51 no PDB 1YD8 . "Complex Of Human Gga3 Gat Domain And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 52 no PDB 1YIW . "X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin" . . . . . 100.00 76 98.68 100.00 2.84e-45 . . . . 18583 1 + 53 no PDB 1YJ1 . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 54 no PDB 1YX5 . "Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX" . . . . . 100.00 98 100.00 100.00 2.31e-46 . . . . 18583 1 + 55 no PDB 1YX6 . "Solution Structure Of S5a Uim-2UBIQUITIN COMPLEX" . . . . . 100.00 98 100.00 100.00 2.31e-46 . . . . 18583 1 + 56 no PDB 1ZGU . "Solution Structure Of The Human Mms2-Ubiquitin Complex" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 57 no PDB 2AYO . "Structure Of Usp14 Bound To Ubquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 58 no PDB 2BGF . "Nmr Structure Of Lys48-Linked Di-Ubiquitin Using Chemical Shift Perturbation Data Together With Rdcs And 15n- Relaxation Data" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 59 no PDB 2C7M . "Human Rabex-5 Residues 1-74 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 60 no PDB 2C7N . "Human Rabex-5 Residues 1-74 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 61 no PDB 2D3G . "Double Sided Ubiquitin Binding Of Hrs-Uim" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 62 no PDB 2DEN . "Solution Structure Of The Ubiquitin-Associated Domain Of Human Bmsc-Ubp And Its Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 63 no PDB 2DX5 . "The Complex Structure Between The Mouse Eap45-Glue Domain And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 64 no PDB 2FCM . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 65 no PDB 2FCN . "X-Ray Crystal Structure Of A Chemically Synthesized [d-Val35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.36e-44 . . . . 18583 1 + 66 no PDB 2FCQ . "X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin With A Cubic Space Group" . . . . . 100.00 76 98.68 100.00 2.84e-45 . . . . 18583 1 + 67 no PDB 2FCS . "X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group" . . . . . 100.00 76 97.37 98.68 3.83e-44 . . . . 18583 1 + 68 no PDB 2FID . "Crystal Structure Of A Bovine Rabex-5 Fragment Complexed With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 69 no PDB 2FIF . "Crystal Structure Of A Bovine Rabex-5 Fragment Complexed With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 70 no PDB 2FUH . "Solution Structure Of The Ubch5cUB NON-Covalent Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 71 no PDB 2G45 . "Co-Crystal Structure Of Znf Ubp Domain From The Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 72 no PDB 2GMI . Mms2UBC13~UBIQUITIN . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 73 no PDB 2HD5 . "Usp2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 74 no PDB 2HTH . "Structural Basis For Ubiquitin Recognition By The Human Eap45ESCRT-Ii Glue Domain" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 75 no PDB 2IBI . "Covalent Ubiquitin-Usp2 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 76 no PDB 2J7Q . "Crystal Structure Of The Ubiquitin-Specific Protease Encoded By Murine Cytomegalovirus Tegument Protein M48 In Complex With A U" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 77 no PDB 2JF5 . "Crystal Structure Of Lys63-Linked Di-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 78 no PDB 2JRI . "Solution Structure Of The Josephin Domain Of Ataxin-3 In Complex With Ubiquitin Molecule." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 79 no PDB 2JY6 . "Solution Structure Of The Complex Of Ubiquitin And Ubiquilin 1 Uba Domain" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 80 no PDB 2JZZ . "Solid-State Nmr Structure Of Microcrystalline Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 81 no PDB 2K25 . "Automated Nmr Structure Of The Ubb By Fapsy" . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 82 no PDB 2K39 . "Recognition Dynamics Up To Microseconds Revealed From Rdc Derived Ubiquitin Ensemble In Solution" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 83 no PDB 2K6D . "Cin85 Sh3-C Domain In Complex With Ubiquitin" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 84 no PDB 2K8B . "Solution Structure Of Plaa Family Ubiquitin Binding Domain (Pfuc) Cis Isomer In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 85 no PDB 2K8C . "Solution Structure Of Plaa Family Ubiquitin Binding Domain (Pfuc) Trans Isomer In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 86 no PDB 2KDE . "Nmr Structure Of Major S5a (196-306):k48 Linked Diubiquitin Species" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 87 no PDB 2KDF . "Nmr Structure Of Minor S5a (196-306):k48 Linked Diubiquitin Species" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 88 no PDB 2KHW . "Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 89 no PDB 2KJH . "Nmr Based Structural Model Of The Ubch8-Ubiquitin Complex" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 90 no PDB 2KLG . "Pere Nmr Structure Of Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 91 no PDB 2KN5 . "A Correspondence Between Solution-State Dynamics Of An Individual Protein And The Sequence And Conformational Diversity Of Its " . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 92 no PDB 2KOX . "Nmr Residual Dipolar Couplings Identify Long Range Correlated Motions In The Backbone Of The Protein Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 93 no PDB 2KTF . "Solution Nmr Structure Of Human Polymerase Iota Ubm2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 94 no PDB 2KWU . "Solution Structure Of Ubm2 Of Murine Polymerase Iota In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 95 no PDB 2KWV . "Solution Structure Of Ubm1 Of Murine Polymerase Iota In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 96 no PDB 2KX0 . "The Solution Structure Of Ubb+1, Frameshift Mutant Of Ubiquitin B" . . . . . 98.68 103 98.67 100.00 6.21e-44 . . . . 18583 1 + 97 no PDB 2L0F . "Solution Nmr Structure Of Human Polymerase Iota Ubm2 (P692a Mutant) In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 98 no PDB 2L0T . "Solution Structure Of The Complex Of Ubiquitin And The Vhs Domain Of Stam2" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 99 no PDB 2L3Z . "Proton-Detected 4d Dream Solid-State Nmr Structure Of Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 100 no PDB 2LD9 . "Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs" . . . . . 100.00 77 100.00 100.00 7.92e-46 . . . . 18583 1 + 101 no PDB 2LJ5 . "Description Of The Structural Fluctuations Of Proteins From Structure- Based Calculations Of Residual Dipolar Couplings" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 102 no PDB 2LVO . "Structure Of The Gp78cue Domain Bound To Monubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 103 no PDB 2LVP . "Gp78cue Domain Bound To The Distal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 104 no PDB 2LVQ . "Gp78cue Domain Bound To The Proximal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 105 no PDB 2LZ6 . "Distinct Ubiquitin Binding Modes Exhibited By Sh3 Domains: Molecular Determinants And Functional Implications" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 106 no PDB 2MBB . "Solution Structure Of The Human Polymerase Iota Ubm1-ubiquitin Complex" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 107 no PDB 2MBH . "Nmr Structure Of Eklf(22-40)/ubiquitin Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 108 no PDB 2MBO . "K11-linked Diubiquitin Average Solution Structure At Ph 6.8, 0 Mm Nacl" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 109 no PDB 2MBQ . "K11-linked Diubiquitin Average Solution Structure At Ph 6.8, 150 Mm Nacl" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 110 no PDB 2MCN . "Distinct Ubiquitin Binding Modes Exhibited By Sh3 Domains: Molecular Determinants And Functional Implications" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 111 no PDB 2MJ5 . "Structure Of The Uba Domain Of Human Nbr1 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 112 no PDB 2MJB . "Solution Nmr Structure Of Ubiquitin Refined Against Dipolar Couplings In 4 Media" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 113 no PDB 2MOR . "A Tensor-free Method For The Structural And Dynamical Refinement Of Proteins Using Residual Dipolar Couplings" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 114 no PDB 2MRE . "Nmr Structure Of The Rad18-ubz/ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 115 no PDB 2MRO . "Structure Of The Complex Of Ubiquitin And The Uba Domain From Dna- Damage-inducible 1 Protein (ddi1)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 116 no PDB 2MSG . "Solid-state Nmr Structure Of Ubiquitin" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 117 no PDB 2MUR . "Solution Structure Of The Human Faap20 Ubz-ubiquitin Complex" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 118 no PDB 2MWS . "Structure Of The Complex Of Ubiquitin And The Ubiquitin-like (ubl) Domain Of Ddi1" . . . . . 100.00 76 98.68 98.68 4.40e-45 . . . . 18583 1 + 119 no PDB 2N2K . "Ensemble Structure Of The Closed State Of Lys63-linked Diubiquitin In The Absence Of A Ligand" . . . . . 93.42 71 100.00 100.00 6.21e-42 . . . . 18583 1 + 120 no PDB 2NR2 . "The Mumo (Minimal Under-Restraining Minimal Over- Restraining) Method For The Determination Of Native States Ensembles Of Prote" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 121 no PDB 2O6V . "Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 122 no PDB 2OJR . "Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag" . . . . . 100.00 111 100.00 100.00 2.29e-45 . . . . 18583 1 + 123 no PDB 2OOB . "Crystal Structure Of The Uba Domain From Cbl-B Ubiquitin Ligase In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 124 no PDB 2PE9 . "Nmr Based Structure Of The Open Conformation Of Lys48- Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tenso" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 125 no PDB 2PEA . "Nmr Based Structure Of The Closed Conformation Of Lys48- Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Ten" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 126 no PDB 2QHO . "Crystal Structure Of The Uba Domain From Edd Ubiquitin Ligase In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 127 no PDB 2RR9 . "The Solution Structure Of The K63-Ub2:tuims Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 128 no PDB 2RSU . "Alternative Structure Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 129 no PDB 2RU6 . "The Pure Alternative State Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 3.54e-45 . . . . 18583 1 + 130 no PDB 2W9N . "Crystal Structure Of Linear Di-Ubiquitin" . . . . . 98.68 152 100.00 100.00 5.62e-44 . . . . 18583 1 + 131 no PDB 2WDT . "Crystal Structure Of Plasmodium Falciparum Uchl3 In Complex With The Suicide Inhibitor Ubvme" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 132 no PDB 2WWZ . "Tab2 Nzf Domain In Complex With Lys63-Linked Di-Ubiquitin, P212121" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 133 no PDB 2WX0 . "Tab2 Nzf Domain In Complex With Lys63-Linked Di-Ubiquitin, P21" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 134 no PDB 2WX1 . "Tab2 Nzf Domain In Complex With Lys63-Linked Tri-Ubiquitin, P212121" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 135 no PDB 2XBB . "Nedd4 Hect:ub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 136 no PDB 2XEW . "Crystal Structure Of K11-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 137 no PDB 2XK5 . "Crystal Structure Of K6-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 138 no PDB 2Y5B . "Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde" . . . . . 98.68 152 100.00 100.00 4.15e-44 . . . . 18583 1 + 139 no PDB 2Z59 . "Complex Structures Of Mouse Rpn13 (22-130aa) And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 140 no PDB 2ZCB . "Crystal Structure Of Ubiquitin P37aP38A" . . . . . 100.00 76 97.37 97.37 3.44e-44 . . . . 18583 1 + 141 no PDB 2ZCC . "Ubiquitin Crystallized Under High Pressure" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 142 no PDB 2ZNV . "Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 143 no PDB 2ZVN . "Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 144 no PDB 2ZVO . "Nemo Cozi Domain In Complex With Diubiquitin In C2 Space Group" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 145 no PDB 3A1Q . "Crystal Structure Of The Mouse Rap80 Uims In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 146 no PDB 3A33 . "Ubch5b~ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 147 no PDB 3A9J . "Crystal Structure Of The Mouse Tab2-Nzf In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 148 no PDB 3A9K . "Crystal Structure Of The Mouse Tab3-Nzf In Complex With Lys63-Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 149 no PDB 3AI5 . "Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein" . . . . . 97.37 307 100.00 100.00 1.64e-41 . . . . 18583 1 + 150 no PDB 3ALB . "Cyclic Lys48-Linked Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 151 no PDB 3AUL . "Crystal Structure Of Wild-Type Lys48-Linked Diubiquitin In An Open Conformation" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 152 no PDB 3AXC . "Crystal Structure Of Linear Diubiquitin" . . . . . 100.00 154 100.00 100.00 5.98e-45 . . . . 18583 1 + 153 no PDB 3B08 . "Crystal Structure Of The Mouse Hoil1-l-nzf In Complex With Linear Di- Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 154 no PDB 3B0A . "Crystal Structure Of The Mouse Hoil1-l-nzf In Complex With Linear Di- Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 155 no PDB 3BY4 . "Structure Of Ovarian Tumor (Otu) Domain In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 156 no PDB 3C0R . "Structure Of Ovarian Tumor (Otu) Domain In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 157 no PDB 3DVG . "Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin" . . . . . 100.00 80 100.00 100.00 8.24e-46 . . . . 18583 1 + 158 no PDB 3DVN . "Crystal Structure Of K63-specific Fab Apu2.16 Bound To K63-linked Di- Ubiquitin" . . . . . 100.00 80 100.00 100.00 8.24e-46 . . . . 18583 1 + 159 no PDB 3EEC . "X-Ray Structure Of Human Ubiquitin Cd(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 160 no PDB 3EFU . "X-Ray Structure Of Human Ubiquitin-Hg(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 161 no PDB 3EHV . "X-Ray Structure Of Human Ubiquitin Zn(Ii) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 162 no PDB 3H1U . "Structure Of Ubiquitin In Complex With Cd Ions" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 163 no PDB 3H7P . "Crystal Structure Of K63-Linked Di-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 164 no PDB 3H7S . "Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture" . . . . . 100.00 76 98.68 98.68 2.81e-43 . . . . 18583 1 + 165 no PDB 3HM3 . "The Structure And Conformation Of Lys-63 Linked Tetra-Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 166 no PDB 3I3T . "Crystal Structure Of Covalent Ubiquitin-usp21 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 167 no PDB 3IFW . "Crystal Structure Of The S18y Variant Of Ubiquitin Carboxy T Hydrolase L1 Bound To Ubiquitin Vinylmethylester." . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 168 no PDB 3IHP . "Covalent Ubiquitin-Usp5 Complex" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 169 no PDB 3JSV . "Crystal Structure Of Mouse Nemo Cozi In Complex With Lys63- Linked Di-Ubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 170 no PDB 3JVZ . E2~ubiquitin-Hect . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 171 no PDB 3JW0 . E2~ubiquitin-Hect . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 172 no PDB 3K9O . "The Crystal Structure Of E2-25k And Ubb+1 Complex" . . . . . 98.68 96 100.00 100.00 1.27e-44 . . . . 18583 1 + 173 no PDB 3K9P . "The Crystal Structure Of E2-25k And Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 174 no PDB 3KVF . "Crystal Structure Of The I93m Mutant Of Ubiquitin Carboxy Te Hydrolase L1 Bound To Ubiquitin Vinylmethylester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 175 no PDB 3KW5 . "Crystal Structure Of Ubiquitin Carboxy Terminal Hydrolase L1 Ubiquitin Vinylmethylester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 176 no PDB 3LDZ . "Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin" . . . . . 96.05 73 100.00 100.00 1.79e-43 . . . . 18583 1 + 177 no PDB 3M3J . "A New Crystal Form Of Lys48-Linked Diubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 178 no PDB 3MHS . "Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 179 no PDB 3MTN . "Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor" . . . . . 88.16 85 98.51 98.51 1.47e-37 . . . . 18583 1 + 180 no PDB 3N30 . "Crystal Structure Of Cubic Zn3-Hub (Human Ubiquitin) Adduct" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 181 no PDB 3N32 . "The Crystal Structure Of Human Ubiquitin Adduct With Zeise's Salt" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 182 no PDB 3NHE . "High Resolution Structure (1.26a) Of Usp2a In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 183 no PDB 3NOB . "Structure Of K11-linked Di-ubiquitin" . . . . . 100.00 78 100.00 100.00 5.38e-46 . . . . 18583 1 + 184 no PDB 3NS8 . "Crystal Structure Of An Open Conformation Of Lys48-Linked Diubiquitin At Ph 7.5" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 185 no PDB 3O65 . "Crystal Structure Of A Josephin-Ubiquitin Complex: Evolutionary Restraints On Ataxin-3 Deubiquitinating Activity" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 186 no PDB 3OFI . "Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 187 no PDB 3OJ3 . "Crystal Structure Of The A20 Znf4 And Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 188 no PDB 3OJ4 . "Crystal Structure Of The A20 Znf4, Ubiquitin And Ubch5a Complex" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 189 no PDB 3ONS . "Crystal Structure Of Human Ubiquitin In A New Crystal Form" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 190 no PDB 3PHD . "Crystal Structure Of Human Hdac6 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 191 no PDB 3PHW . "Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In Complex With Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 192 no PDB 3PRM . "Structural Analysis Of A Viral Otu Domain Protease From The Crimean- Congo Hemorrhagic Fever Virus In Complex With Human Ubiqui" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 193 no PDB 3PRP . "Structural Analysis Of A Viral Otu Domain Protease From The Crimean- Congo Hemorrhagic Fever Virus In Complex With Human Ubiqui" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 194 no PDB 3PT2 . "Structure Of A Viral Otu Domain Protease Bound To Ubiquitin" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 195 no PDB 3PTF . "X-Ray Structure Of The Non-Covalent Complex Between Ubch5a And Ubiquitin" . . . . . 100.00 79 100.00 100.00 6.66e-46 . . . . 18583 1 + 196 no PDB 3Q3F . "Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnas" . . . . . 98.68 189 100.00 100.00 5.35e-44 . . . . 18583 1 + 197 no PDB 3RUL . "New Strategy To Analyze Structures Of Glycopeptide-Target Complexes" . . . . . 98.68 79 100.00 100.00 3.97e-45 . . . . 18583 1 + 198 no PDB 3TBL . "Structure Of Mono-ubiquitinated Pcna: Implications For Dna Polymerase Switching And Okazaki Fragment Maturation" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 199 no PDB 3TMP . "The Catalytic Domain Of Human Deubiquitinase Duba In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 200 no PDB 3U30 . "Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin" . . . . . 100.00 172 100.00 100.00 6.89e-45 . . . . 18583 1 + 201 no PDB 3UGB . "Ubch5c~ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 202 no PDB 3VDZ . "Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms" . . . . . 100.00 111 100.00 100.00 1.47e-45 . . . . 18583 1 + 203 no PDB 3VFK . "The Structure Of Monodechloro-teicoplanin In Complex With Its Ligand, Using Ubiquitin As A Ligand Carrier" . . . . . 98.68 79 100.00 100.00 3.97e-45 . . . . 18583 1 + 204 no PDB 3VHT . "Crystal Structure Of Gfp-Wrnip1 Ubz Domain Fusion Protein In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 205 no PDB 3VUW . "Crystal Structure Of A20 Zf7 In Complex With Linear Ubiquitin, Form I" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 206 no PDB 3VUX . "Crystal Structure Of A20 Zf7 In Complex With Linear Ubiquitin, Form Ii" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 207 no PDB 3VUY . "Crystal Structure Of A20 Zf7 In Complex With Linear Tetraubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 208 no PDB 3WWQ . "Crystal Structure Of Faap20 Ubz Domain In Complex With Lys63-linked Diubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 209 no PDB 3WXE . "Crystal Structure Of Cyld Usp Domain (c596s) In Complex With Met1- Linked Diubiquitin" . . . . . 94.74 148 100.00 100.00 9.19e-42 . . . . 18583 1 + 210 no PDB 3WXF . "Crystal Structure Of Cyld Usp Domain (c596s E674q) In Complex With Met1-linked Diubiquitin" . . . . . 94.74 148 100.00 100.00 9.19e-42 . . . . 18583 1 + 211 no PDB 3WXG . "Crystal Structure Of Cyld Usp Domain (c596a) In Complex With Lys63- Linked Diubiquitin" . . . . . 94.74 72 100.00 100.00 8.52e-43 . . . . 18583 1 + 212 no PDB 3ZLZ . "Lys6-linked Tri-ubiquitin" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 213 no PDB 3ZNH . "Crimean Congo Hemorrhagic Fever Virus Otu Domain In Complex With Ubiquitin-propargyl." . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 214 no PDB 3ZNI . "Structure Of Phosphotyr363-cbl-b - Ubch5b-ub - Zap-70 Peptide Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 215 no PDB 3ZNZ . "Crystal Structure Of Otulin Otu Domain (c129a) In Complex With Met1-di Ubiquitin" . . . . . 100.00 152 100.00 100.00 6.43e-45 . . . . 18583 1 + 216 no PDB 4A18 . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 217 no PDB 4A19 . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 2" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 218 no PDB 4A1B . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 3" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 219 no PDB 4A1D . "T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 4" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 220 no PDB 4ADX . "The Cryo-em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6" . . . . . 100.00 129 97.37 98.68 2.69e-44 . . . . 18583 1 + 221 no PDB 4AP4 . "Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 222 no PDB 4AUQ . "Structure Of Birc7-Ubch5b-Ub Complex." . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 223 no PDB 4BBN . "Nedd4 Hect-ub:ub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 224 no PDB 4BOS . "Structure Of Otud2 Otu Domain In Complex With Ubiquitin K11- Linked Peptide" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 225 no PDB 4BOZ . "Structure Of Otud2 Otu Domain In Complex With K11-linked Di Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 226 no PDB 4BVU . "Structure Of Shigella Effector Ospg In Complex With Host Ubch5c-ubiquitin Conjugate" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 227 no PDB 4CXC . "Regulation Of The Mammalian Elongation Cycle By 40s Subunit Rolling: A Eukaryotic-specific Ribosome Rearrangement" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 228 no PDB 4CXD . "Regulation Of The Mammalian Elongation Cycle By 40s Subunit Rolling: A Eukaryotic-specific Ribosome Rearrangement" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 229 no PDB 4D5L . "Cryo-em Structures Of Ribosomal 80s Complexes With Termination Factors And Cricket Paralysis Virus Ires Reveal The Ires In The " . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 230 no PDB 4D61 . "Cryo-em Structures Of Ribosomal 80s Complexes With Termination Factors And Cricket Paralysis Virus Ires Reveal The Ires In The " . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 231 no PDB 4DDG . "Crystal Structure Of Human Otub1UBCH5B~UBUB" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 232 no PDB 4DDI . "Crystal Structure Of Human Otub1UBCH5B~UBUB" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 233 no PDB 4DHJ . "The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub Complex" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 234 no PDB 4DHZ . "The Structure Of HCEOTUB1-Ubiquitin Aldehyde-Ubc13~ub" . . . . . 98.68 76 100.00 100.00 3.99e-45 . . . . 18583 1 + 235 no PDB 4FJV . "Crystal Structure Of Human Otubain2 And Ubiquitin Complex" . . . . . 100.00 86 100.00 100.00 9.86e-46 . . . . 18583 1 + 236 no PDB 4HXD . "Diversity Of Ubiquitin And Isg15 Specificity Amongst Nairoviruses Viral Ovarian Tumor Domain Proteases" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 237 no PDB 4I6N . "Crystal Structure Of Trichinella Spiralis Uch37 Catalytic Domain Bound To Ubiquitin Vinyl Methyl Ester" . . . . . 97.37 75 100.00 100.00 4.54e-44 . . . . 18583 1 + 238 no PDB 4IG7 . "Crystal Structure Of Trichinella Spiralis Uch37 Bound To Ubiquitin Vinyl Methyl Ester" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 239 no PDB 4IUM . "Equine Arteritis Virus Papain-like Protease 2 (plp2) Covalently Bound To Ubiquitin" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 240 no PDB 4JIO . "Bro1 V Domain And Ubiquitin" . . . . . 100.00 76 98.68 98.68 4.85e-45 . . . . 18583 1 + 241 no PDB 4JQW . "Crystal Structure Of A Complex Of Nod1 Card And Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 242 no PDB 4K1R . "Crystal Structure Of Schizosaccharomyces Pombe Sst2 Catalytic Domain And Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 243 no PDB 4K7S . "Crystal Structure Of Zn2-hub (human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 244 no PDB 4K7U . "Crystal Structure Of Zn2.3-hub (human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 245 no PDB 4K7W . "Crystal Structure Of Zn3-hub(human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 246 no PDB 4KSK . "Gumby/fam105b In Complex With Ubiquitin" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 247 no PDB 4KSL . "Gumby/fam105b In Complex With Linear Di-ubiquitin" . . . . . 100.00 156 100.00 100.00 6.34e-45 . . . . 18583 1 + 248 no PDB 4KZX . "Rabbit 40s Ribosomal Subunit In Complex With Eif1." . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 249 no PDB 4KZY . "Rabbit 40s Ribosomal Subunit In Complex With Eif1 And Eif1a." . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 250 no PDB 4KZZ . "Rabbit 40s Ribosomal Subunit In Complex With Mrna, Initiator Trna And Eif1a" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 251 no PDB 4LCD . "Structure Of An Rsp5xubxsna3 Complex: Mechanism Of Ubiquitin Ligation And Lysine Prioritization By A Hect E3" . . . . . 97.37 83 100.00 100.00 1.79e-44 . . . . 18583 1 + 252 no PDB 4LDT . "The Structure Of H/ceotub1-ubiquitin Aldehyde-ubch5b~ub" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 253 no PDB 4LJO . "Structure Of An Active Ligase (hoip)/ubiquitin Transfer Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 254 no PDB 4LJP . "Structure Of An Active Ligase (hoip-h889a)/ubiquitin Transfer Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 255 no PDB 4M0W . "Crystal Structure Of Sars-cov Papain-like Protease C112s Mutant In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 256 no PDB 4MDK . "Cdc34-ubiquitin-cc0651 Complex" . . . . . 100.00 80 100.00 100.00 6.85e-46 . . . . 18583 1 + 257 no PDB 4MM3 . "Crystal Structure Of Sars-cov Papain-like Protease Plpro In Complex With Ubiquitin Aldehyde" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 258 no PDB 4MSM . "Crystal Structure Of Schizosaccharomyces Pombe Amsh-like Protease Sst2 E286a Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 259 no PDB 4MSQ . "Crystal Structure Of Schizosaccharomyces Pombe Amsh-like Protease Sst2 Catalytic Domain Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 260 no PDB 4NQK . "Structure Of An Ubiquitin Complex" . . . . . 100.00 79 100.00 100.00 1.20e-45 . . . . 18583 1 + 261 no PDB 4NQL . "The Crystal Structure Of The Dub Domain Of Amsh Orthologue, Sst2 From S. Pombe, In Complex With Lysine 63-linked Diubiquitin" . . . . . 100.00 77 100.00 100.00 7.42e-46 . . . . 18583 1 + 262 no PDB 4P4H . "Caught-in-action Signaling Complex Of Rig-i 2card Domain And Mavs Card Domain" . . . . . 100.00 79 100.00 100.00 1.20e-45 . . . . 18583 1 + 263 no PDB 4PIG . "Crystal Structure Of The Ubiquitin K11s Mutant" . . . . . 100.00 76 98.68 98.68 2.81e-45 . . . . 18583 1 + 264 no PDB 4PIH . "X-ray Crystal Structure Of The K33s Mutant Of Ubiquitin" . . . . . 100.00 76 98.68 98.68 2.81e-45 . . . . 18583 1 + 265 no PDB 4PIJ . "X-ray Crystal Structure Of The K11s/k63s Double Mutant Of Ubiquitin" . . . . . 98.68 75 97.33 97.33 7.90e-44 . . . . 18583 1 + 266 no PDB 4PQT . "Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Co-crystal Structures Of Enzyme With Substrate And" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 267 no PDB 4R62 . "Structure Of Rad6~ub" . . . . . 100.00 78 100.00 100.00 6.20e-46 . . . . 18583 1 + 268 no PDB 4RF0 . "Crystal Structure Of The Middle-east Respiratory Syndrome Coronavirus Papain-like Protease In Complex With Ubiquitin (space Gro" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 269 no PDB 4RF1 . "Crystal Structure Of The Middle-east Respiratory Syndrome Coronavirus Papain-like Protease In Complex With Ubiquitin (space Gro" . . . . . 98.68 75 100.00 100.00 4.28e-45 . . . . 18583 1 + 270 no PDB 4S1Z . "Crystal Structure Of Trabid Nzf1 In Complex With K29 Linked Di- Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 271 no PDB 4S22 . "Crystal Structure Of K29 Linked Di-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 272 no PDB 4UEL . "Uch-l5 In Complex With Ubiquitin-propargyl Bound To The Rpn13 Deubad Domain" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 273 no PDB 4UF6 . "Uch-l5 In Complex With Ubiquitin-propargyl Bound To An Activating Fragment Of Ino80g" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 274 no PDB 4UN2 . "Crystal Structure Of The Uba Domain Of Dsk2 In Complex With Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 275 no PDB 4UPX . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Pre-like State" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 276 no PDB 4UQ1 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Post-like State" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 277 no PDB 4UQ4 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Post-like State" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 278 no PDB 4UQ5 . "Mammalian 80s Hcv-ires Initiation Complex With Eif5b Pre-like State" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 279 no PDB 4V3K . "Rnf38-ubch5b-ub Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 280 no PDB 4V3L . "Rnf38-ub-ubch5b-ub Complex" . . . . . 100.00 81 100.00 100.00 7.68e-46 . . . . 18583 1 + 281 no PDB 4W20 . "Structure Of The Mammalian 60s Ribosomal Subunit (this Entry Contains The Large Ribosomal Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 282 no PDB 4W22 . "Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 283 no PDB 4W23 . "Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Small Ribosomal Subunit)" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 284 no PDB 4W25 . "Structure Of The Idle Mammalian Ribosome-sec61 Complex (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 285 no PDB 4W27 . "Structure Of The Translating Mammalian Ribosome-sec61 Complex (this Entry Contains The Large Ribosomal Subunit Proteins)" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 286 no PDB 4W28 . "Structure Of The Translating Mammalian Ribosome-sec61 Complex (this Entry Contains The Small Ribosomal Subunit)" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 287 no PDB 4WHV . Rnf8/ubc13c87k~ub . . . . . 100.00 83 100.00 100.00 1.61e-45 . . . . 18583 1 + 288 no PDB 4WLR . "Crystal Structure Of Much37-hrpn13 Ctd-hub Complex" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 289 no PDB 4WUR . "The Crystal Structure Of The Mers-cov Papain-like Protease (c111s) With Human Ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 290 no PDB 4WZP . "Ser65 Phosphorylated Ubiquitin, Major Conformation" . . . . . 100.00 76 98.68 98.68 4.64e-45 . . . . 18583 1 + 291 no PDB 4XKL . "Crystal Structure Of Ndp52 Zf2 In Complex With Mono-ubiquitin" . . . . . 100.00 80 100.00 100.00 1.02e-45 . . . . 18583 1 + 292 no PDB 4XOF . "Observing The Overall Rocking Motion Of A Protein In A Crystal - Orthorhombic Ubiquitin Crystals Without Zinc." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 293 no PDB 4XOK . "Observing The Overall Rocking Motion Of A Protein In A Crystal." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 294 no PDB 4XOL . "Observing The Overall Rocking Motion Of A Protein In A Crystal - Cubic Ubiquitin Crystals." . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 295 no PDB 4XYZ . "Crystal Structure Of K33 Linked Di-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 296 no PDB 4Y1H . "Crystal Structure Of K33 Linked Tri-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 297 no PDB 4Z9S . "Non-covalent Assembly Of Monoubiquitin That Mimics K11 Poly-ubiquitin" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 298 no PDB 4ZFR . "Catalytic Domain Of Sst2 F403a Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 299 no PDB 4ZFT . "Catalytic Domain Of Sst2 F403w Mutant Bound To Ubiquitin" . . . . . 100.00 81 100.00 100.00 1.15e-45 . . . . 18583 1 + 300 no PDB 4ZPZ . "Crystal Structure Of Semi-synthetic Ubiquitin With Phospho-ser65 And Ala46cys" . . . . . 100.00 76 97.37 97.37 1.81e-44 . . . . 18583 1 + 301 no PDB 5A5B . "Structure Of The 26s Proteasome-ubp6 Complex" . . . . . 98.68 76 100.00 100.00 4.40e-45 . . . . 18583 1 + 302 no PDB 5AF4 . "Structure Of Lys33-linked Diub" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 303 no PDB 5AF5 . "Structure Of Lys33-linked Triub S.g. P 212121" . . . . . 96.05 73 98.63 100.00 5.42e-43 . . . . 18583 1 + 304 no PDB 5AF6 . "Structure Of Lys33-linked Diub Bound To Trabid Nzf1" . . . . . 100.00 76 98.68 100.00 1.56e-45 . . . . 18583 1 + 305 no PDB 5AIT . "A Complex Of Of Rnf4-ring Domain, Ubev2, Ubc13-ub (isopeptide Crosslink)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 306 no PDB 5AIU . "A Complex Of Rnf4-ring Domain, Ubc13-ub (isopeptide Crosslink)" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 307 no PDB 5CAW . "Structure Of Pediculus Humanus Parkin Bound To Phospho-ubiquitin" . . . . . 98.68 76 98.67 98.67 2.77e-44 . . . . 18583 1 + 308 no DBJ BAA03983 . "polyubiquitin [Rattus norvegicus]" . . . . . 100.00 305 100.00 100.00 3.25e-43 . . . . 18583 1 + 309 no DBJ BAA09860 . "polyubiquitin [Homo sapiens]" . . . . . 100.00 611 98.68 98.68 1.53e-40 . . . . 18583 1 + 310 no DBJ BAA11842 . "ubiquitin [Cavia porcellus]" . . . . . 100.00 311 100.00 100.00 3.52e-43 . . . . 18583 1 + 311 no DBJ BAA11843 . "ubiquitin extention protein [Cavia porcellus]" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 312 no DBJ BAA23486 . "polyubiquitin [Homo sapiens]" . . . . . 100.00 609 98.68 98.68 8.23e-41 . . . . 18583 1 + 313 no EMBL CAA25706 . "unnamed protein product [Saccharomyces cerevisiae]" . . . . . 50.00 191 100.00 100.00 4.38e-16 . . . . 18583 1 + 314 no EMBL CAA26488 . "unnamed protein product [Gallus gallus]" . . . . . 100.00 157 98.68 98.68 3.90e-44 . . . . 18583 1 + 315 no EMBL CAA28495 . "ubiquitin [Homo sapiens]" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 316 no EMBL CAA30183 . "unnamed protein product [Dictyostelium discoideum]" . . . . . 100.00 128 97.37 97.37 7.90e-44 . . . . 18583 1 + 317 no EMBL CAA30815 . "unnamed protein product [Cricetulus sp.]" . . . . . 93.42 223 100.00 100.00 5.43e-40 . . . . 18583 1 + 318 no GB AAA02769 . "polyprotein [Bovine viral diarrhea virus 1-Osloss]" . . . . . 98.68 3975 97.33 100.00 2.69e-39 . . . . 18583 1 + 319 no GB AAA28154 . "polyubiquitin [Caenorhabditis elegans]" . . . . . 100.00 838 97.37 98.68 1.06e-39 . . . . 18583 1 + 320 no GB AAA28997 . "ubiquitin [Drosophila melanogaster]" . . . . . 100.00 231 100.00 100.00 4.85e-44 . . . . 18583 1 + 321 no GB AAA28998 . "ubiquitin-hybrid protein precursor [Drosophila melanogaster]" . . . . . 100.00 156 100.00 100.00 1.42e-45 . . . . 18583 1 + 322 no GB AAA28999 . "ubiquitin, partial [Drosophila melanogaster]" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 323 no PIR I50437 . "polyubiquitin 4 - chicken [Gallus gallus]" . . . . . 100.00 305 100.00 100.00 3.25e-43 . . . . 18583 1 + 324 no PIR I51568 . "polyubiquitin - African clawed frog (fragment)" . . . . . 100.00 167 100.00 100.00 1.00e-44 . . . . 18583 1 + 325 no PIR I65237 . "ubiquitin / ribosomal protein L40, cytosolic [validated] - rat" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 326 no PIR JN0790 . "ubiquitin/ribosomal protein CEP52 fusion protein - Leishmania major" . . . . . 100.00 128 97.37 98.68 3.43e-45 . . . . 18583 1 + 327 no PIR S13928 . "ubiquitin precursor - chicken [Gallus gallus]" . . . . . 100.00 229 100.00 100.00 5.35e-44 . . . . 18583 1 + 328 no PRF 0412265A . ubiquitin . . . . . 98.68 75 98.67 98.67 1.80e-44 . . . . 18583 1 + 329 no PRF 1101405A . "ubiquitin precursor" . . . . . 50.00 191 100.00 100.00 4.33e-16 . . . . 18583 1 + 330 no PRF 1212243A . "ubiquitin S1" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 331 no PRF 1212243B . "ubiquitin S5" . . . . . 92.11 77 98.57 98.57 1.12e-40 . . . . 18583 1 + 332 no PRF 1212243C . "ubiquitin S3" . . . . . 100.00 76 100.00 100.00 6.54e-46 . . . . 18583 1 + 333 no REF NP_001005123 . "ubiquitin-60S ribosomal protein L40 [Xenopus (Silurana) tropicalis]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 334 no REF NP_001006688 . "ubiquitin C [Xenopus (Silurana) tropicalis]" . . . . . 100.00 609 100.00 100.00 1.45e-41 . . . . 18583 1 + 335 no REF NP_001009117 . "polyubiquitin-B [Pan troglodytes]" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 336 no REF NP_001009202 . "polyubiquitin-B [Ovis aries]" . . . . . 100.00 305 98.68 100.00 5.72e-43 . . . . 18583 1 + 337 no REF NP_001009286 . "ubiquitin-60S ribosomal protein L40 [Ovis aries]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 338 no SP P0C273 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 339 no SP P0C275 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 340 no SP P0C276 . "RecName: Full=Ubiquitin-60S ribosomal protein L40; AltName: Full=Ubiquitin A-52 residue ribosomal protein fusion product 1; Con" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + 341 no SP P0CG47 . "RecName: Full=Polyubiquitin-B; Contains: RecName: Full=Ubiquitin; Flags: Precursor" . . . . . 100.00 229 100.00 100.00 5.18e-44 . . . . 18583 1 + 342 no SP P0CG48 . "RecName: Full=Polyubiquitin-C; Contains: RecName: Full=Ubiquitin; Flags: Precursor" . . . . . 100.00 685 100.00 100.00 2.13e-41 . . . . 18583 1 + 343 no TPD FAA00319 . "TPA: polyubiquitin [Cryptococcus neoformans var. neoformans B-3501A]" . . . . . 100.00 456 97.37 98.68 1.11e-40 . . . . 18583 1 + 344 no TPE CEL68433 . "TPA: ubiquitin / ribosomal protein CEP52 fusion protein, putative [Neospora caninum Liverpool]" . . . . . 100.00 129 98.68 100.00 1.60e-45 . . . . 18583 1 + 345 no TPE CEL70397 . "TPA: Ubiquitin, related [Neospora caninum Liverpool]" . . . . . 100.00 535 98.68 100.00 3.17e-41 . . . . 18583 1 + 346 no TPE CEL75964 . "TPA: ubiquitin / ribosomal protein CEP52 fusion protein, putative [Toxoplasma gondii VEG]" . . . . . 100.00 129 98.68 100.00 1.60e-45 . . . . 18583 1 + 347 no TPE CEL78064 . "TPA: polyubiquitin, putative [Toxoplasma gondii VEG]" . . . . . 100.00 307 98.68 100.00 1.16e-42 . . . . 18583 1 + 348 no TPG DAA18802 . "TPA: polyubiquitin [Bos taurus]" . . . . . 100.00 305 100.00 100.00 3.43e-43 . . . . 18583 1 + 349 no TPG DAA20663 . "TPA: ubiquitin C [Bos taurus]" . . . . . 98.68 314 98.67 100.00 1.30e-41 . . . . 18583 1 + 350 no TPG DAA20672 . "TPA: ubiquitin B-like [Bos taurus]" . . . . . 100.00 77 98.68 98.68 4.88e-45 . . . . 18583 1 + 351 no TPG DAA24675 . "TPA: 40S ribosomal protein S27a [Bos taurus]" . . . . . 100.00 156 100.00 100.00 7.65e-46 . . . . 18583 1 + 352 no TPG DAA28295 . "TPA: ubiquitin and ribosomal protein L40 [Bos taurus]" . . . . . 100.00 128 100.00 100.00 4.55e-46 . . . . 18583 1 + + stop_ + + loop_ + _Entity_comp_index.ID + _Entity_comp_index.Auth_seq_ID + _Entity_comp_index.Comp_ID + _Entity_comp_index.Comp_label + _Entity_comp_index.Entry_ID + _Entity_comp_index.Entity_ID + + 1 . MET . 18583 1 + 2 . GLN . 18583 1 + 3 . ILE . 18583 1 + 4 . PHE . 18583 1 + 5 . VAL . 18583 1 + 6 . LYS . 18583 1 + 7 . THR . 18583 1 + 8 . LEU . 18583 1 + 9 . THR . 18583 1 + 10 . GLY . 18583 1 + 11 . LYS . 18583 1 + 12 . THR . 18583 1 + 13 . ILE . 18583 1 + 14 . THR . 18583 1 + 15 . LEU . 18583 1 + 16 . GLU . 18583 1 + 17 . VAL . 18583 1 + 18 . GLU . 18583 1 + 19 . PRO . 18583 1 + 20 . SER . 18583 1 + 21 . ASP . 18583 1 + 22 . THR . 18583 1 + 23 . ILE . 18583 1 + 24 . GLU . 18583 1 + 25 . ASN . 18583 1 + 26 . VAL . 18583 1 + 27 . LYS . 18583 1 + 28 . ALA . 18583 1 + 29 . LYS . 18583 1 + 30 . ILE . 18583 1 + 31 . GLN . 18583 1 + 32 . ASP . 18583 1 + 33 . LYS . 18583 1 + 34 . GLU . 18583 1 + 35 . GLY . 18583 1 + 36 . ILE . 18583 1 + 37 . PRO . 18583 1 + 38 . PRO . 18583 1 + 39 . ASP . 18583 1 + 40 . GLN . 18583 1 + 41 . GLN . 18583 1 + 42 . ARG . 18583 1 + 43 . LEU . 18583 1 + 44 . ILE . 18583 1 + 45 . PHE . 18583 1 + 46 . ALA . 18583 1 + 47 . GLY . 18583 1 + 48 . LYS . 18583 1 + 49 . GLN . 18583 1 + 50 . LEU . 18583 1 + 51 . GLU . 18583 1 + 52 . ASP . 18583 1 + 53 . GLY . 18583 1 + 54 . ARG . 18583 1 + 55 . THR . 18583 1 + 56 . LEU . 18583 1 + 57 . SER . 18583 1 + 58 . ASP . 18583 1 + 59 . TYR . 18583 1 + 60 . ASN . 18583 1 + 61 . ILE . 18583 1 + 62 . GLN . 18583 1 + 63 . LYS . 18583 1 + 64 . GLU . 18583 1 + 65 . SER . 18583 1 + 66 . THR . 18583 1 + 67 . LEU . 18583 1 + 68 . HIS . 18583 1 + 69 . LEU . 18583 1 + 70 . VAL . 18583 1 + 71 . LEU . 18583 1 + 72 . ARG . 18583 1 + 73 . LEU . 18583 1 + 74 . ARG . 18583 1 + 75 . GLY . 18583 1 + 76 . GLY . 18583 1 + + stop_ + + loop_ + _Entity_poly_seq.Hetero + _Entity_poly_seq.Mon_ID + _Entity_poly_seq.Num + _Entity_poly_seq.Comp_index_ID + _Entity_poly_seq.Entry_ID + _Entity_poly_seq.Entity_ID + + . MET 1 1 18583 1 + . GLN 2 2 18583 1 + . ILE 3 3 18583 1 + . PHE 4 4 18583 1 + . VAL 5 5 18583 1 + . LYS 6 6 18583 1 + . THR 7 7 18583 1 + . LEU 8 8 18583 1 + . THR 9 9 18583 1 + . GLY 10 10 18583 1 + . LYS 11 11 18583 1 + . THR 12 12 18583 1 + . ILE 13 13 18583 1 + . THR 14 14 18583 1 + . LEU 15 15 18583 1 + . GLU 16 16 18583 1 + . VAL 17 17 18583 1 + . GLU 18 18 18583 1 + . PRO 19 19 18583 1 + . SER 20 20 18583 1 + . ASP 21 21 18583 1 + . THR 22 22 18583 1 + . ILE 23 23 18583 1 + . GLU 24 24 18583 1 + . ASN 25 25 18583 1 + . VAL 26 26 18583 1 + . LYS 27 27 18583 1 + . ALA 28 28 18583 1 + . LYS 29 29 18583 1 + . ILE 30 30 18583 1 + . GLN 31 31 18583 1 + . ASP 32 32 18583 1 + . LYS 33 33 18583 1 + . GLU 34 34 18583 1 + . GLY 35 35 18583 1 + . ILE 36 36 18583 1 + . PRO 37 37 18583 1 + . PRO 38 38 18583 1 + . ASP 39 39 18583 1 + . GLN 40 40 18583 1 + . GLN 41 41 18583 1 + . ARG 42 42 18583 1 + . LEU 43 43 18583 1 + . ILE 44 44 18583 1 + . PHE 45 45 18583 1 + . ALA 46 46 18583 1 + . GLY 47 47 18583 1 + . LYS 48 48 18583 1 + . GLN 49 49 18583 1 + . LEU 50 50 18583 1 + . GLU 51 51 18583 1 + . ASP 52 52 18583 1 + . GLY 53 53 18583 1 + . ARG 54 54 18583 1 + . THR 55 55 18583 1 + . LEU 56 56 18583 1 + . SER 57 57 18583 1 + . ASP 58 58 18583 1 + . TYR 59 59 18583 1 + . ASN 60 60 18583 1 + . ILE 61 61 18583 1 + . GLN 62 62 18583 1 + . LYS 63 63 18583 1 + . GLU 64 64 18583 1 + . SER 65 65 18583 1 + . THR 66 66 18583 1 + . LEU 67 67 18583 1 + . HIS 68 68 18583 1 + . LEU 69 69 18583 1 + . VAL 70 70 18583 1 + . LEU 71 71 18583 1 + . ARG 72 72 18583 1 + . LEU 73 73 18583 1 + . ARG 74 74 18583 1 + . GLY 75 75 18583 1 + . GLY 76 76 18583 1 + + stop_ + +save_ + + +save_entity_2 + _Entity.Sf_category entity + _Entity.Sf_framecode entity_2 + _Entity.Entry_ID 18583 + _Entity.ID 2 + _Entity.BMRB_code . + _Entity.Name gp78CUE + _Entity.Type polymer + _Entity.Polymer_common_type . + _Entity.Polymer_type polypeptide(L) + _Entity.Polymer_type_details . + _Entity.Polymer_strand_ID C + _Entity.Polymer_seq_one_letter_code_can . + _Entity.Polymer_seq_one_letter_code +; +SNSQLNAMAHQIQEMFPQVP +YHLVLQDLQLTRSVEITTDN +ILEGRIQVPFPT +; + _Entity.Target_identifier . + _Entity.Polymer_author_defined_seq . + _Entity.Polymer_author_seq_details . + _Entity.Ambiguous_conformational_states no + _Entity.Ambiguous_chem_comp_sites no + _Entity.Nstd_monomer no + _Entity.Nstd_chirality no + _Entity.Nstd_linkage no + _Entity.Nonpolymer_comp_ID . + _Entity.Nonpolymer_comp_label . + _Entity.Number_of_monomers 52 + _Entity.Number_of_nonpolymer_components . + _Entity.Paramagnetic no + _Entity.Thiol_state 'not present' + _Entity.Src_method man + _Entity.Parent_entity_ID . + _Entity.Fragment . + _Entity.Mutation . + _Entity.EC_number . + _Entity.Calc_isoelectric_point . + _Entity.Formula_weight 5966.808 + _Entity.Formula_weight_exptl . + _Entity.Formula_weight_exptl_meth . + _Entity.Details . + _Entity.DB_query_date . + _Entity.DB_query_revised_last_date 2015-01-30 + + loop_ + _Entity_db_link.Ordinal + _Entity_db_link.Author_supplied + _Entity_db_link.Database_code + _Entity_db_link.Accession_code + _Entity_db_link.Entry_mol_code + _Entity_db_link.Entry_mol_name + _Entity_db_link.Entry_experimental_method + _Entity_db_link.Entry_structure_resolution + _Entity_db_link.Entry_relation_type + _Entity_db_link.Entry_details + _Entity_db_link.Chimera_segment_ID + _Entity_db_link.Seq_query_to_submitted_percent + _Entity_db_link.Seq_subject_length + _Entity_db_link.Seq_identity + _Entity_db_link.Seq_positive + _Entity_db_link.Seq_homology_expectation_val + _Entity_db_link.Seq_align_begin + _Entity_db_link.Seq_align_end + _Entity_db_link.Seq_difference_details + _Entity_db_link.Seq_alignment_details + _Entity_db_link.Entry_ID + _Entity_db_link.Entity_ID + + 1 no BMRB 18581 . entity . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 2 no BMRB 18582 . gp78CUE . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 3 no BMRB 18584 . gp78CUE . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 4 no PDB 2EJS . "Solution Structure Of Ruh-076, A Human Cue Domain" . . . . . 96.15 58 100.00 100.00 2.71e-27 . . . . 18583 2 + 5 no PDB 2LVN . "Structure Of The Gp78 Cue Domain" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 6 no PDB 2LVO . "Structure Of The Gp78cue Domain Bound To Monubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 7 no PDB 2LVP . "Gp78cue Domain Bound To The Distal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 8 no PDB 2LVQ . "Gp78cue Domain Bound To The Proximal Ubiquitin Of K48-Linked Diubiquitin" . . . . . 100.00 52 100.00 100.00 1.65e-28 . . . . 18583 2 + 9 no PDB 4G3O . "Crystal Structure Of The Cue Domain Of The E3 Ubiquitin Ligase Amfr (Gp78)" . . . . . 84.62 58 97.73 97.73 9.44e-22 . . . . 18583 2 + 10 no DBJ BAE01277 . "unnamed protein product [Macaca fascicularis]" . . . . . 100.00 552 100.00 100.00 3.33e-26 . . . . 18583 2 + 11 no DBJ BAE34049 . "unnamed protein product [Mus musculus]" . . . . . 100.00 643 98.08 100.00 1.44e-25 . . . . 18583 2 + 12 no DBJ BAE41974 . "unnamed protein product [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 13 no DBJ BAK63135 . "autocrine motility factor receptor, isoform 2 [Pan troglodytes]" . . . . . 100.00 548 100.00 100.00 3.46e-26 . . . . 18583 2 + 14 no GB AAD56721 . "autocrine motility factor receptor [Mus musculus]" . . . . . 100.00 643 98.08 100.00 1.32e-25 . . . . 18583 2 + 15 no GB AAD56722 . "autocrine motility factor receptor [Homo sapiens]" . . . . . 100.00 643 100.00 100.00 8.27e-26 . . . . 18583 2 + 16 no GB AAH03256 . "Amfr protein, partial [Mus musculus]" . . . . . 100.00 244 98.08 100.00 4.16e-27 . . . . 18583 2 + 17 no GB AAH17043 . "AMFR protein, partial [Homo sapiens]" . . . . . 100.00 292 100.00 100.00 4.77e-27 . . . . 18583 2 + 18 no GB AAH34538 . "Autocrine motility factor receptor [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 19 no REF NP_001039439 . "E3 ubiquitin-protein ligase AMFR [Bos taurus]" . . . . . 100.00 645 100.00 100.00 7.86e-26 . . . . 18583 2 + 20 no REF NP_001135 . "E3 ubiquitin-protein ligase AMFR [Homo sapiens]" . . . . . 100.00 643 100.00 100.00 7.72e-26 . . . . 18583 2 + 21 no REF NP_001267243 . "E3 ubiquitin-protein ligase AMFR [Pan troglodytes]" . . . . . 100.00 548 100.00 100.00 3.46e-26 . . . . 18583 2 + 22 no REF NP_035917 . "E3 ubiquitin-protein ligase AMFR [Mus musculus]" . . . . . 100.00 639 98.08 100.00 1.43e-25 . . . . 18583 2 + 23 no REF XP_001091030 . "PREDICTED: autocrine motility factor receptor, isoform 2 [Macaca mulatta]" . . . . . 100.00 552 100.00 100.00 3.20e-26 . . . . 18583 2 + 24 no SP Q9R049 . "RecName: Full=E3 ubiquitin-protein ligase AMFR; AltName: Full=Autocrine motility factor receptor; Short=AMF receptor [Mus muscu" . . . . . 100.00 643 98.08 100.00 1.44e-25 . . . . 18583 2 + 25 no SP Q9UKV5 . "RecName: Full=E3 ubiquitin-protein ligase AMFR; AltName: Full=Autocrine motility factor receptor; Short=AMF receptor; AltName: " . . . . . 100.00 643 100.00 100.00 7.72e-26 . . . . 18583 2 + 26 no TPG DAA20037 . "TPA: autocrine motility factor receptor [Bos taurus]" . . . . . 100.00 590 100.00 100.00 7.80e-26 . . . . 18583 2 + + stop_ + + loop_ + _Entity_comp_index.ID + _Entity_comp_index.Auth_seq_ID + _Entity_comp_index.Comp_ID + _Entity_comp_index.Comp_label + _Entity_comp_index.Entry_ID + _Entity_comp_index.Entity_ID + + 1 453 SER . 18583 2 + 2 454 ASN . 18583 2 + 3 455 SER . 18583 2 + 4 456 GLN . 18583 2 + 5 457 LEU . 18583 2 + 6 458 ASN . 18583 2 + 7 459 ALA . 18583 2 + 8 460 MET . 18583 2 + 9 461 ALA . 18583 2 + 10 462 HIS . 18583 2 + 11 463 GLN . 18583 2 + 12 464 ILE . 18583 2 + 13 465 GLN . 18583 2 + 14 466 GLU . 18583 2 + 15 467 MET . 18583 2 + 16 468 PHE . 18583 2 + 17 469 PRO . 18583 2 + 18 470 GLN . 18583 2 + 19 471 VAL . 18583 2 + 20 472 PRO . 18583 2 + 21 473 TYR . 18583 2 + 22 474 HIS . 18583 2 + 23 475 LEU . 18583 2 + 24 476 VAL . 18583 2 + 25 477 LEU . 18583 2 + 26 478 GLN . 18583 2 + 27 479 ASP . 18583 2 + 28 480 LEU . 18583 2 + 29 481 GLN . 18583 2 + 30 482 LEU . 18583 2 + 31 483 THR . 18583 2 + 32 484 ARG . 18583 2 + 33 485 SER . 18583 2 + 34 486 VAL . 18583 2 + 35 487 GLU . 18583 2 + 36 488 ILE . 18583 2 + 37 489 THR . 18583 2 + 38 490 THR . 18583 2 + 39 491 ASP . 18583 2 + 40 492 ASN . 18583 2 + 41 493 ILE . 18583 2 + 42 494 LEU . 18583 2 + 43 495 GLU . 18583 2 + 44 496 GLY . 18583 2 + 45 497 ARG . 18583 2 + 46 498 ILE . 18583 2 + 47 499 GLN . 18583 2 + 48 500 VAL . 18583 2 + 49 501 PRO . 18583 2 + 50 502 PHE . 18583 2 + 51 503 PRO . 18583 2 + 52 504 THR . 18583 2 + + stop_ + + loop_ + _Entity_poly_seq.Hetero + _Entity_poly_seq.Mon_ID + _Entity_poly_seq.Num + _Entity_poly_seq.Comp_index_ID + _Entity_poly_seq.Entry_ID + _Entity_poly_seq.Entity_ID + + . SER 1 1 18583 2 + . ASN 2 2 18583 2 + . SER 3 3 18583 2 + . GLN 4 4 18583 2 + . LEU 5 5 18583 2 + . ASN 6 6 18583 2 + . ALA 7 7 18583 2 + . MET 8 8 18583 2 + . ALA 9 9 18583 2 + . HIS 10 10 18583 2 + . GLN 11 11 18583 2 + . ILE 12 12 18583 2 + . GLN 13 13 18583 2 + . GLU 14 14 18583 2 + . MET 15 15 18583 2 + . PHE 16 16 18583 2 + . PRO 17 17 18583 2 + . GLN 18 18 18583 2 + . VAL 19 19 18583 2 + . PRO 20 20 18583 2 + . TYR 21 21 18583 2 + . HIS 22 22 18583 2 + . LEU 23 23 18583 2 + . VAL 24 24 18583 2 + . LEU 25 25 18583 2 + . GLN 26 26 18583 2 + . ASP 27 27 18583 2 + . LEU 28 28 18583 2 + . GLN 29 29 18583 2 + . LEU 30 30 18583 2 + . THR 31 31 18583 2 + . ARG 32 32 18583 2 + . SER 33 33 18583 2 + . VAL 34 34 18583 2 + . GLU 35 35 18583 2 + . ILE 36 36 18583 2 + . THR 37 37 18583 2 + . THR 38 38 18583 2 + . ASP 39 39 18583 2 + . ASN 40 40 18583 2 + . ILE 41 41 18583 2 + . LEU 42 42 18583 2 + . GLU 43 43 18583 2 + . GLY 44 44 18583 2 + . ARG 45 45 18583 2 + . ILE 46 46 18583 2 + . GLN 47 47 18583 2 + . VAL 48 48 18583 2 + . PRO 49 49 18583 2 + . PHE 50 50 18583 2 + . PRO 51 51 18583 2 + . THR 52 52 18583 2 + + stop_ + +save_ + + + #################### + # Natural source # + #################### + +save_natural_source + _Entity_natural_src_list.Sf_category natural_source + _Entity_natural_src_list.Sf_framecode natural_source + _Entity_natural_src_list.Entry_ID 18583 + _Entity_natural_src_list.ID 1 + + loop_ + _Entity_natural_src.ID + _Entity_natural_src.Entity_ID + _Entity_natural_src.Entity_label + _Entity_natural_src.Entity_chimera_segment_ID + _Entity_natural_src.NCBI_taxonomy_ID + _Entity_natural_src.Type + _Entity_natural_src.Common + _Entity_natural_src.Organism_name_scientific + _Entity_natural_src.Organism_name_common + _Entity_natural_src.Organism_acronym + _Entity_natural_src.ICTVdb_decimal_code + _Entity_natural_src.Superkingdom + _Entity_natural_src.Kingdom + _Entity_natural_src.Genus + _Entity_natural_src.Species + _Entity_natural_src.Strain + _Entity_natural_src.Variant + _Entity_natural_src.Subvariant + _Entity_natural_src.Organ + _Entity_natural_src.Tissue + _Entity_natural_src.Tissue_fraction + _Entity_natural_src.Cell_line + _Entity_natural_src.Cell_type + _Entity_natural_src.ATCC_number + _Entity_natural_src.Organelle + _Entity_natural_src.Cellular_location + _Entity_natural_src.Fragment + _Entity_natural_src.Fraction + _Entity_natural_src.Secretion + _Entity_natural_src.Plasmid + _Entity_natural_src.Plasmid_details + _Entity_natural_src.Gene_mnemonic + _Entity_natural_src.Dev_stage + _Entity_natural_src.Details + _Entity_natural_src.Citation_ID + _Entity_natural_src.Citation_label + _Entity_natural_src.Entry_ID + _Entity_natural_src.Entity_natural_src_list_ID + + 1 1 $entity_1 . 9606 organism . 'Homo sapiens' Human . . Eukaryota Metazoa Homo sapiens . . . . . . . . . . . . . . . . . . . . . 18583 1 + 2 2 $entity_2 . 9606 organism . 'Homo sapiens' Human . . Eukaryota Metazoa Homo sapiens . . . . . . . . . . . . . . . . . . . . . 18583 1 + + stop_ + +save_ + + + ######################### + # Experimental source # + ######################### + +save_experimental_source + _Entity_experimental_src_list.Sf_category experimental_source + _Entity_experimental_src_list.Sf_framecode experimental_source + _Entity_experimental_src_list.Entry_ID 18583 + _Entity_experimental_src_list.ID 1 + + loop_ + _Entity_experimental_src.ID + _Entity_experimental_src.Entity_ID + _Entity_experimental_src.Entity_label + _Entity_experimental_src.Entity_chimera_segment_ID + _Entity_experimental_src.Production_method + _Entity_experimental_src.Host_org_scientific_name + _Entity_experimental_src.Host_org_name_common + _Entity_experimental_src.Host_org_details + _Entity_experimental_src.Host_org_NCBI_taxonomy_ID + _Entity_experimental_src.Host_org_genus + _Entity_experimental_src.Host_org_species + _Entity_experimental_src.Host_org_strain + _Entity_experimental_src.Host_org_variant + _Entity_experimental_src.Host_org_subvariant + _Entity_experimental_src.Host_org_organ + _Entity_experimental_src.Host_org_tissue + _Entity_experimental_src.Host_org_tissue_fraction + _Entity_experimental_src.Host_org_cell_line + _Entity_experimental_src.Host_org_cell_type + _Entity_experimental_src.Host_org_cellular_location + _Entity_experimental_src.Host_org_organelle + _Entity_experimental_src.Host_org_gene + _Entity_experimental_src.Host_org_culture_collection + _Entity_experimental_src.Host_org_ATCC_number + _Entity_experimental_src.Vector_type + _Entity_experimental_src.PDBview_host_org_vector_name + _Entity_experimental_src.PDBview_plasmid_name + _Entity_experimental_src.Vector_name + _Entity_experimental_src.Vector_details + _Entity_experimental_src.Vendor_name + _Entity_experimental_src.Host_org_dev_stage + _Entity_experimental_src.Details + _Entity_experimental_src.Citation_ID + _Entity_experimental_src.Citation_label + _Entity_experimental_src.Entry_ID + _Entity_experimental_src.Entity_experimental_src_list_ID + + 1 1 $entity_1 . 'recombinant technology' 'Escherichia coli' . . . Escherichia coli . . . . . . . . . . . . . . . . pET3a . . . . . . 18583 1 + 2 2 $entity_2 . 'recombinant technology' 'Escherichia coli' . . . Escherichia coli . . . . . . . . . . . . . . . . pET3a . . . . . . 18583 1 + + stop_ + +save_ + + +##################################### +# Sample contents and methodology # +##################################### + + ######################## + # Sample description # + ######################## + +save_sample_1 + _Sample.Sf_category sample + _Sample.Sf_framecode sample_1 + _Sample.Entry_ID 18583 + _Sample.ID 1 + _Sample.Type solution + _Sample.Sub_type . + _Sample.Details +; +50 mM Tris pH 7.2 +50mM NaCl +; + _Sample.Aggregate_sample_number . + _Sample.Solvent_system '90% H2O/10% D2O' + _Sample.Preparation_date . + _Sample.Preparation_expiration_date . + _Sample.Polycrystallization_protocol . + _Sample.Single_crystal_protocol . + _Sample.Crystal_grow_apparatus . + _Sample.Crystal_grow_atmosphere . + _Sample.Crystal_grow_details . + _Sample.Crystal_grow_method . + _Sample.Crystal_grow_method_cit_ID . + _Sample.Crystal_grow_pH . + _Sample.Crystal_grow_pH_range . + _Sample.Crystal_grow_pressure . + _Sample.Crystal_grow_pressure_esd . + _Sample.Crystal_grow_seeding . + _Sample.Crystal_grow_seeding_cit_ID . + _Sample.Crystal_grow_temp . + _Sample.Crystal_grow_temp_details . + _Sample.Crystal_grow_temp_esd . + _Sample.Crystal_grow_time . + _Sample.Oriented_sample_prep_protocol . + _Sample.Lyophilization_cryo_protectant . + _Sample.Storage_protocol . + + loop_ + _Sample_component.ID + _Sample_component.Mol_common_name + _Sample_component.Isotopic_labeling + _Sample_component.Assembly_ID + _Sample_component.Assembly_label + _Sample_component.Entity_ID + _Sample_component.Entity_label + _Sample_component.Product_ID + _Sample_component.Type + _Sample_component.Concentration_val + _Sample_component.Concentration_val_min + _Sample_component.Concentration_val_max + _Sample_component.Concentration_val_units + _Sample_component.Concentration_val_err + _Sample_component.Vendor + _Sample_component.Vendor_product_name + _Sample_component.Vendor_product_code + _Sample_component.Entry_ID + _Sample_component.Sample_ID + + 1 TRIS 'natural abundance' . . . . . . 50 . . mM . . . . 18583 1 + 2 'sodium chloride' 'natural abundance' . . . . . . 50 . . mM . . . . 18583 1 + 3 H2O 'natural abundance' . . . . . . 90 . . % . . . . 18583 1 + 4 D2O 'natural abundance' . . . . . . 10 . . % . . . . 18583 1 + + stop_ + +save_ + + +####################### +# Sample conditions # +####################### + +save_sample_conditions_1 + _Sample_condition_list.Sf_category sample_conditions + _Sample_condition_list.Sf_framecode sample_conditions_1 + _Sample_condition_list.Entry_ID 18583 + _Sample_condition_list.ID 1 + _Sample_condition_list.Details . + + loop_ + _Sample_condition_variable.Type + _Sample_condition_variable.Val + _Sample_condition_variable.Val_err + _Sample_condition_variable.Val_units + _Sample_condition_variable.Entry_ID + _Sample_condition_variable.Sample_condition_list_ID + + pH 7.2 . pH 18583 1 + pressure 1 . atm 18583 1 + temperature 298 . K 18583 1 + + stop_ + +save_ + + +############################ +# Computer software used # +############################ + +save_SPARKY + _Software.Sf_category software + _Software.Sf_framecode SPARKY + _Software.Entry_ID 18583 + _Software.ID 1 + _Software.Name SPARKY + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + Goddard . . 18583 1 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + 'chemical shift assignment' 18583 1 + 'peak picking' 18583 1 + + stop_ + +save_ + + +save_NMRPipe + _Software.Sf_category software + _Software.Sf_framecode NMRPipe + _Software.Entry_ID 18583 + _Software.ID 2 + _Software.Name NMRPipe + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . 18583 2 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + processing 18583 2 + + stop_ + +save_ + + +save_CNS + _Software.Sf_category software + _Software.Sf_framecode CNS + _Software.Entry_ID 18583 + _Software.ID 3 + _Software.Name CNS + _Software.Version . + _Software.Details . + + loop_ + _Vendor.Name + _Vendor.Address + _Vendor.Electronic_address + _Vendor.Entry_ID + _Vendor.Software_ID + + 'Alexandre Bonvin' . . 18583 3 + + stop_ + + loop_ + _Task.Task + _Task.Entry_ID + _Task.Software_ID + + 'structure solution' 18583 3 + + stop_ + +save_ + + +######################### +# Experimental detail # +######################### + + ################################## + # NMR Spectrometer definitions # + ################################## + +save_spectrometer_1 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_1 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 1 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Bruker + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 600 + +save_ + + +save_spectrometer_2 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_2 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 2 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Bruker + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 700 + +save_ + + +save_spectrometer_3 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_3 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 3 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Varian + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 600 + +save_ + + +save_spectrometer_4 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode spectrometer_4 + _NMR_spectrometer.Entry_ID 18583 + _NMR_spectrometer.ID 4 + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer Varian + _NMR_spectrometer.Model INOVA + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength 800 + +save_ + + +save_NMR_spectrometer_list + _NMR_spectrometer_list.Sf_category NMR_spectrometer_list + _NMR_spectrometer_list.Sf_framecode NMR_spectrometer_list + _NMR_spectrometer_list.Entry_ID 18583 + _NMR_spectrometer_list.ID 1 + + loop_ + _NMR_spectrometer_view.ID + _NMR_spectrometer_view.Name + _NMR_spectrometer_view.Manufacturer + _NMR_spectrometer_view.Model + _NMR_spectrometer_view.Serial_number + _NMR_spectrometer_view.Field_strength + _NMR_spectrometer_view.Details + _NMR_spectrometer_view.Citation_ID + _NMR_spectrometer_view.Citation_label + _NMR_spectrometer_view.Entry_ID + _NMR_spectrometer_view.NMR_spectrometer_list_ID + + 1 spectrometer_1 Bruker INOVA . 600 . . . 18583 1 + 2 spectrometer_2 Bruker INOVA . 700 . . . 18583 1 + 3 spectrometer_3 Varian INOVA . 600 . . . 18583 1 + 4 spectrometer_4 Varian INOVA . 800 . . . 18583 1 + + stop_ + +save_ + + + ############################# + # NMR applied experiments # + ############################# + +save_experiment_list + _Experiment_list.Sf_category experiment_list + _Experiment_list.Sf_framecode experiment_list + _Experiment_list.Entry_ID 18583 + _Experiment_list.ID 1 + _Experiment_list.Details . + + loop_ + _Experiment.ID + _Experiment.Name + _Experiment.Raw_data_flag + _Experiment.NMR_spec_expt_ID + _Experiment.NMR_spec_expt_label + _Experiment.MS_expt_ID + _Experiment.MS_expt_label + _Experiment.SAXS_expt_ID + _Experiment.SAXS_expt_label + _Experiment.FRET_expt_ID + _Experiment.FRET_expt_label + _Experiment.EMR_expt_ID + _Experiment.EMR_expt_label + _Experiment.Sample_ID + _Experiment.Sample_label + _Experiment.Sample_state + _Experiment.Sample_volume + _Experiment.Sample_volume_units + _Experiment.Sample_condition_list_ID + _Experiment.Sample_condition_list_label + _Experiment.Sample_spinning_rate + _Experiment.Sample_angle + _Experiment.NMR_tube_type + _Experiment.NMR_spectrometer_ID + _Experiment.NMR_spectrometer_label + _Experiment.NMR_spectrometer_probe_ID + _Experiment.NMR_spectrometer_probe_label + _Experiment.NMR_spectral_processing_ID + _Experiment.NMR_spectral_processing_label + _Experiment.Mass_spectrometer_ID + _Experiment.Mass_spectrometer_label + _Experiment.Xray_instrument_ID + _Experiment.Xray_instrument_label + _Experiment.Fluorescence_instrument_ID + _Experiment.Fluorescence_instrument_label + _Experiment.EMR_instrument_ID + _Experiment.EMR_instrument_label + _Experiment.Chromatographic_system_ID + _Experiment.Chromatographic_system_label + _Experiment.Chromatographic_column_ID + _Experiment.Chromatographic_column_label + _Experiment.Entry_ID + _Experiment.Experiment_list_ID + + 1 '2D 1H-15N HSQC' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 2 '2D 1H-13C HSQC' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 3 '3D HNCO' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 4 '3D CBCA(CO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 5 '3D C(CO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 6 '3D H(CCO)NH' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 7 '3D HNCACB' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 8 '2D 1H-13C HSQC aromatic' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + 9 '3D 1H-15N NOESY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . . . . . . . . . . . . . . . . . . . 18583 1 + + stop_ + +save_ + + +#################### +# NMR parameters # +#################### + + ############################## + # Assigned chemical shifts # + ############################## + + ################################ + # Chemical shift referencing # + ################################ + +save_chemical_shift_reference_1 + _Chem_shift_reference.Sf_category chem_shift_reference + _Chem_shift_reference.Sf_framecode chemical_shift_reference_1 + _Chem_shift_reference.Entry_ID 18583 + _Chem_shift_reference.ID 1 + _Chem_shift_reference.Details . + + loop_ + _Chem_shift_ref.Atom_type + _Chem_shift_ref.Atom_isotope_number + _Chem_shift_ref.Mol_common_name + _Chem_shift_ref.Atom_group + _Chem_shift_ref.Concentration_val + _Chem_shift_ref.Concentration_units + _Chem_shift_ref.Solvent + _Chem_shift_ref.Rank + _Chem_shift_ref.Chem_shift_units + _Chem_shift_ref.Chem_shift_val + _Chem_shift_ref.Ref_method + _Chem_shift_ref.Ref_type + _Chem_shift_ref.Indirect_shift_ratio + _Chem_shift_ref.External_ref_loc + _Chem_shift_ref.External_ref_sample_geometry + _Chem_shift_ref.External_ref_axis + _Chem_shift_ref.Indirect_shift_ratio_cit_ID + _Chem_shift_ref.Indirect_shift_ratio_cit_label + _Chem_shift_ref.Ref_correction_type + _Chem_shift_ref.Correction_val + _Chem_shift_ref.Correction_val_cit_ID + _Chem_shift_ref.Correction_val_cit_label + _Chem_shift_ref.Entry_ID + _Chem_shift_ref.Chem_shift_reference_ID + + C 13 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.251449530 . . . . . . . . . 18583 1 + H 1 DSS 'methyl protons' . . . . ppm 0.00 internal direct 1.000000000 . . . . . . . . . 18583 1 + N 15 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.101329118 . . . . . . . . . 18583 1 + P 31 DSS 'methyl protons' . . . . ppm 0.00 na indirect 0.404808636 . . . . . . . . . 18583 1 + + stop_ + +save_ + + + ################################### + # Assigned chemical shift lists # + ################################### + +################################################################### +# Chemical Shift Ambiguity Index Value Definitions # +# # +# The values other than 1 are used for those atoms with different # +# chemical shifts that cannot be assigned to stereospecific atoms # +# or to specific residues or chains. # +# # +# Index Value Definition # +# # +# 1 Unique (including isolated methyl protons, # +# geminal atoms, and geminal methyl # +# groups with identical chemical shifts) # +# (e.g. ILE HD11, HD12, HD13 protons) # +# 2 Ambiguity of geminal atoms or geminal methyl # +# proton groups (e.g. ASP HB2 and HB3 # +# protons, LEU CD1 and CD2 carbons, or # +# LEU HD11, HD12, HD13 and HD21, HD22, # +# HD23 methyl protons) # +# 3 Aromatic atoms on opposite sides of # +# symmetrical rings (e.g. TYR HE1 and HE2 # +# protons) # +# 4 Intraresidue ambiguities (e.g. LYS HG and # +# HD protons or TRP HZ2 and HZ3 protons) # +# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # +# 6 Intermolecular ambiguities (e.g. ASP 31 CA # +# in monomer 1 and ASP 31 CA in monomer 2 # +# of an asymmetrical homodimer, duplex # +# DNA assignments, or other assignments # +# that may apply to atoms in one or more # +# molecule in the molecular assembly) # +# 9 Ambiguous, specific ambiguity not defined # +# # +################################################################### +save_gp78CUE_amides_in_gp78-K48Ub2 + _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts + _Assigned_chem_shift_list.Sf_framecode gp78CUE_amides_in_gp78-K48Ub2 + _Assigned_chem_shift_list.Entry_ID 18583 + _Assigned_chem_shift_list.ID 1 + _Assigned_chem_shift_list.Sample_condition_list_ID 1 + _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 + _Assigned_chem_shift_list.Chem_shift_reference_ID 1 + _Assigned_chem_shift_list.Chem_shift_reference_label $chemical_shift_reference_1 + _Assigned_chem_shift_list.Chem_shift_1H_err 0.05 + _Assigned_chem_shift_list.Chem_shift_13C_err 0.5 + _Assigned_chem_shift_list.Chem_shift_15N_err 0.2 + _Assigned_chem_shift_list.Chem_shift_31P_err . + _Assigned_chem_shift_list.Chem_shift_2H_err . + _Assigned_chem_shift_list.Chem_shift_19F_err . + _Assigned_chem_shift_list.Error_derivation_method . + _Assigned_chem_shift_list.Details . + _Assigned_chem_shift_list.Text_data_format . + _Assigned_chem_shift_list.Text_data . + + loop_ + _Chem_shift_experiment.Experiment_ID + _Chem_shift_experiment.Experiment_name + _Chem_shift_experiment.Sample_ID + _Chem_shift_experiment.Sample_label + _Chem_shift_experiment.Sample_state + _Chem_shift_experiment.Entry_ID + _Chem_shift_experiment.Assigned_chem_shift_list_ID + + 1 '2D 1H-15N HSQC' . . . 18583 1 + 4 '3D CBCA(CO)NH' . . . 18583 1 + 7 '3D HNCACB' . . . 18583 1 + + stop_ + + loop_ + _Atom_chem_shift.ID + _Atom_chem_shift.Assembly_atom_ID + _Atom_chem_shift.Entity_assembly_ID + _Atom_chem_shift.Entity_ID + _Atom_chem_shift.Comp_index_ID + _Atom_chem_shift.Seq_ID + _Atom_chem_shift.Comp_ID + _Atom_chem_shift.Atom_ID + _Atom_chem_shift.Atom_type + _Atom_chem_shift.Atom_isotope_number + _Atom_chem_shift.Val + _Atom_chem_shift.Val_err + _Atom_chem_shift.Assign_fig_of_merit + _Atom_chem_shift.Ambiguity_code + _Atom_chem_shift.Occupancy + _Atom_chem_shift.Resonance_ID + _Atom_chem_shift.Auth_entity_assembly_ID + _Atom_chem_shift.Auth_asym_ID + _Atom_chem_shift.Auth_seq_ID + _Atom_chem_shift.Auth_comp_ID + _Atom_chem_shift.Auth_atom_ID + _Atom_chem_shift.Details + _Atom_chem_shift.Entry_ID + _Atom_chem_shift.Assigned_chem_shift_list_ID + + 1 . 1 1 2 2 GLN H H 1 8.98 0.05 . 1 . . . A 2 GLN H . 18583 1 + 2 . 1 1 2 2 GLN N N 15 122.96 0.20 . 1 . . . A 2 GLN N . 18583 1 + 3 . 1 1 3 3 ILE H H 1 8.27 0.05 . 1 . . . A 3 ILE H . 18583 1 + 4 . 1 1 3 3 ILE N N 15 114.84 0.20 . 1 . . . A 3 ILE N . 18583 1 + 5 . 1 1 4 4 PHE H H 1 8.56 0.05 . 1 . . . A 4 PHE H . 18583 1 + 6 . 1 1 4 4 PHE N N 15 118.78 0.20 . 1 . . . A 4 PHE N . 18583 1 + 7 . 1 1 5 5 VAL H H 1 9.35 0.05 . 1 . . . A 5 VAL H . 18583 1 + 8 . 1 1 5 5 VAL N N 15 120.88 0.20 . 1 . . . A 5 VAL N . 18583 1 + 9 . 1 1 6 6 LYS H H 1 9.05 0.05 . 1 . . . A 6 LYS H . 18583 1 + 10 . 1 1 6 6 LYS N N 15 128.64 0.20 . 1 . . . A 6 LYS N . 18583 1 + 11 . 1 1 7 7 THR H H 1 8.72 0.05 . 1 . . . A 7 THR H . 18583 1 + 12 . 1 1 7 7 THR N N 15 115.08 0.20 . 1 . . . A 7 THR N . 18583 1 + 13 . 1 1 8 8 LEU H H 1 9.34 0.05 . 1 . . . A 8 LEU H . 18583 1 + 14 . 1 1 8 8 LEU N N 15 121.97 0.20 . 1 . . . A 8 LEU N . 18583 1 + 15 . 1 1 9 9 THR H H 1 7.65 0.05 . 1 . . . A 9 THR H . 18583 1 + 16 . 1 1 9 9 THR N N 15 105.77 0.20 . 1 . . . A 9 THR N . 18583 1 + 17 . 1 1 10 10 GLY H H 1 7.82 0.05 . 1 . . . A 10 GLY H . 18583 1 + 18 . 1 1 10 10 GLY N N 15 109.42 0.20 . 1 . . . A 10 GLY N . 18583 1 + 19 . 1 1 11 11 LYS H H 1 7.33 0.05 . 1 . . . A 11 LYS H . 18583 1 + 20 . 1 1 11 11 LYS N N 15 122.48 0.20 . 1 . . . A 11 LYS N . 18583 1 + 21 . 1 1 12 12 THR H H 1 8.66 0.05 . 1 . . . A 12 THR H . 18583 1 + 22 . 1 1 12 12 THR N N 15 120.93 0.20 . 1 . . . A 12 THR N . 18583 1 + 23 . 1 1 13 13 ILE H H 1 9.72 0.05 . 1 . . . A 13 ILE H . 18583 1 + 24 . 1 1 13 13 ILE N N 15 129.80 0.20 . 1 . . . A 13 ILE N . 18583 1 + 25 . 1 1 14 14 THR H H 1 8.81 0.05 . 1 . . . A 14 THR H . 18583 1 + 26 . 1 1 14 14 THR N N 15 123.06 0.20 . 1 . . . A 14 THR N . 18583 1 + 27 . 1 1 15 15 LEU H H 1 8.68 0.05 . 1 . . . A 15 LEU H . 18583 1 + 28 . 1 1 15 15 LEU N N 15 125.43 0.20 . 1 . . . A 15 LEU N . 18583 1 + 29 . 1 1 16 16 GLU H H 1 8.13 0.05 . 1 . . . A 16 GLU H . 18583 1 + 30 . 1 1 16 16 GLU N N 15 122.68 0.20 . 1 . . . A 16 GLU N . 18583 1 + 31 . 1 1 17 17 VAL H H 1 8.96 0.05 . 1 . . . A 17 VAL H . 18583 1 + 32 . 1 1 17 17 VAL N N 15 117.75 0.20 . 1 . . . A 17 VAL N . 18583 1 + 33 . 1 1 18 18 GLU H H 1 8.65 0.05 . 1 . . . A 18 GLU H . 18583 1 + 34 . 1 1 18 18 GLU N N 15 119.32 0.20 . 1 . . . A 18 GLU N . 18583 1 + 35 . 1 1 20 20 SER H H 1 7.03 0.05 . 1 . . . A 20 SER H . 18583 1 + 36 . 1 1 20 20 SER N N 15 103.43 0.20 . 1 . . . A 20 SER N . 18583 1 + 37 . 1 1 21 21 ASP H H 1 8.08 0.05 . 1 . . . A 21 ASP H . 18583 1 + 38 . 1 1 21 21 ASP N N 15 124.19 0.20 . 1 . . . A 21 ASP N . 18583 1 + 39 . 1 1 22 22 THR H H 1 7.89 0.05 . 1 . . . A 22 THR H . 18583 1 + 40 . 1 1 22 22 THR N N 15 109.14 0.20 . 1 . . . A 22 THR N . 18583 1 + 41 . 1 1 23 23 ILE H H 1 8.56 0.05 . 1 . . . A 23 ILE H . 18583 1 + 42 . 1 1 23 23 ILE N N 15 121.79 0.20 . 1 . . . A 23 ILE N . 18583 1 + 43 . 1 1 24 24 GLU H H 1 8.48 0.05 . 1 . . . A 24 GLU H . 18583 1 + 44 . 1 1 24 24 GLU N N 15 121.73 0.20 . 1 . . . A 24 GLU N . 18583 1 + 45 . 1 1 25 25 ASN H H 1 7.95 0.05 . 1 . . . A 25 ASN H . 18583 1 + 46 . 1 1 25 25 ASN N N 15 121.25 0.20 . 1 . . . A 25 ASN N . 18583 1 + 47 . 1 1 26 26 VAL H H 1 8.16 0.05 . 1 . . . A 26 VAL H . 18583 1 + 48 . 1 1 26 26 VAL N N 15 122.46 0.20 . 1 . . . A 26 VAL N . 18583 1 + 49 . 1 1 27 27 LYS H H 1 8.53 0.05 . 1 . . . A 27 LYS H . 18583 1 + 50 . 1 1 27 27 LYS N N 15 119.23 0.20 . 1 . . . A 27 LYS N . 18583 1 + 51 . 1 1 28 28 ALA H H 1 7.99 0.05 . 1 . . . A 28 ALA H . 18583 1 + 52 . 1 1 28 28 ALA N N 15 123.09 0.20 . 1 . . . A 28 ALA N . 18583 1 + 53 . 1 1 29 29 LYS H H 1 7.93 0.05 . 1 . . . A 29 LYS H . 18583 1 + 54 . 1 1 29 29 LYS N N 15 120.64 0.20 . 1 . . . A 29 LYS N . 18583 1 + 55 . 1 1 30 30 ILE H H 1 8.29 0.05 . 1 . . . A 30 ILE H . 18583 1 + 56 . 1 1 30 30 ILE N N 15 121.76 0.20 . 1 . . . A 30 ILE N . 18583 1 + 57 . 1 1 31 31 GLN H H 1 8.53 0.05 . 1 . . . A 31 GLN H . 18583 1 + 58 . 1 1 31 31 GLN N N 15 123.81 0.20 . 1 . . . A 31 GLN N . 18583 1 + 59 . 1 1 32 32 ASP H H 1 8.12 0.05 . 1 . . . A 32 ASP H . 18583 1 + 60 . 1 1 32 32 ASP N N 15 120.19 0.20 . 1 . . . A 32 ASP N . 18583 1 + 61 . 1 1 33 33 LYS H H 1 7.48 0.05 . 1 . . . A 33 LYS H . 18583 1 + 62 . 1 1 33 33 LYS N N 15 115.87 0.20 . 1 . . . A 33 LYS N . 18583 1 + 63 . 1 1 34 34 GLU H H 1 8.71 0.05 . 1 . . . A 34 GLU H . 18583 1 + 64 . 1 1 34 34 GLU N N 15 114.03 0.20 . 1 . . . A 34 GLU N . 18583 1 + 65 . 1 1 36 36 ILE H H 1 6.12 0.05 . 1 . . . A 36 ILE H . 18583 1 + 66 . 1 1 36 36 ILE N N 15 120.80 0.20 . 1 . . . A 36 ILE N . 18583 1 + 67 . 1 1 39 39 ASP H H 1 8.57 0.05 . 1 . . . A 39 ASP H . 18583 1 + 68 . 1 1 39 39 ASP N N 15 113.90 0.20 . 1 . . . A 39 ASP N . 18583 1 + 69 . 1 1 40 40 GLN H H 1 7.80 0.05 . 1 . . . A 40 GLN H . 18583 1 + 70 . 1 1 40 40 GLN N N 15 116.92 0.20 . 1 . . . A 40 GLN N . 18583 1 + 71 . 1 1 41 41 GLN H H 1 7.52 0.05 . 1 . . . A 41 GLN H . 18583 1 + 72 . 1 1 41 41 GLN N N 15 117.92 0.20 . 1 . . . A 41 GLN N . 18583 1 + 73 . 1 1 43 43 LEU H H 1 8.81 0.05 . 1 . . . A 43 LEU H . 18583 1 + 74 . 1 1 43 43 LEU N N 15 123.75 0.20 . 1 . . . A 43 LEU N . 18583 1 + 75 . 1 1 44 44 ILE H H 1 9.27 0.05 . 1 . . . A 44 ILE H . 18583 1 + 76 . 1 1 44 44 ILE N N 15 123.21 0.20 . 1 . . . A 44 ILE N . 18583 1 + 77 . 1 1 45 45 PHE H H 1 8.82 0.05 . 1 . . . A 45 PHE H . 18583 1 + 78 . 1 1 45 45 PHE N N 15 124.80 0.20 . 1 . . . A 45 PHE N . 18583 1 + 79 . 1 1 46 46 ALA H H 1 8.72 0.05 . 1 . . . A 46 ALA H . 18583 1 + 80 . 1 1 46 46 ALA N N 15 133.01 0.20 . 1 . . . A 46 ALA N . 18583 1 + 81 . 1 1 48 48 LYS H H 1 8.56 0.05 . 1 . . . A 48 LYS H . 18583 1 + 82 . 1 1 48 48 LYS N N 15 124.90 0.20 . 1 . . . A 48 LYS N . 18583 1 + 83 . 1 1 50 50 LEU H H 1 8.74 0.05 . 1 . . . A 50 LEU H . 18583 1 + 84 . 1 1 50 50 LEU N N 15 126.43 0.20 . 1 . . . A 50 LEU N . 18583 1 + 85 . 1 1 51 51 GLU H H 1 8.49 0.05 . 1 . . . A 51 GLU H . 18583 1 + 86 . 1 1 51 51 GLU N N 15 123.28 0.20 . 1 . . . A 51 GLU N . 18583 1 + 87 . 1 1 52 52 ASP H H 1 8.20 0.05 . 1 . . . A 52 ASP H . 18583 1 + 88 . 1 1 52 52 ASP N N 15 120.85 0.20 . 1 . . . A 52 ASP N . 18583 1 + 89 . 1 1 54 54 ARG H H 1 7.46 0.05 . 1 . . . A 54 ARG H . 18583 1 + 90 . 1 1 54 54 ARG N N 15 119.64 0.20 . 1 . . . A 54 ARG N . 18583 1 + 91 . 1 1 55 55 THR H H 1 8.81 0.05 . 1 . . . A 55 THR H . 18583 1 + 92 . 1 1 55 55 THR N N 15 108.82 0.20 . 1 . . . A 55 THR N . 18583 1 + 93 . 1 1 56 56 LEU H H 1 8.14 0.05 . 1 . . . A 56 LEU H . 18583 1 + 94 . 1 1 56 56 LEU N N 15 118.15 0.20 . 1 . . . A 56 LEU N . 18583 1 + 95 . 1 1 57 57 SER H H 1 8.48 0.05 . 1 . . . A 57 SER H . 18583 1 + 96 . 1 1 57 57 SER N N 15 113.52 0.20 . 1 . . . A 57 SER N . 18583 1 + 97 . 1 1 58 58 ASP H H 1 7.97 0.05 . 1 . . . A 58 ASP H . 18583 1 + 98 . 1 1 58 58 ASP N N 15 124.93 0.20 . 1 . . . A 58 ASP N . 18583 1 + 99 . 1 1 59 59 TYR H H 1 7.21 0.05 . 1 . . . A 59 TYR H . 18583 1 + 100 . 1 1 59 59 TYR N N 15 115.77 0.20 . 1 . . . A 59 TYR N . 18583 1 + 101 . 1 1 60 60 ASN H H 1 8.16 0.05 . 1 . . . A 60 ASN H . 18583 1 + 102 . 1 1 60 60 ASN N N 15 115.93 0.20 . 1 . . . A 60 ASN N . 18583 1 + 103 . 1 1 61 61 ILE H H 1 7.34 0.05 . 1 . . . A 61 ILE H . 18583 1 + 104 . 1 1 61 61 ILE N N 15 119.34 0.20 . 1 . . . A 61 ILE N . 18583 1 + 105 . 1 1 62 62 GLN H H 1 7.65 0.05 . 1 . . . A 62 GLN H . 18583 1 + 106 . 1 1 62 62 GLN N N 15 125.07 0.20 . 1 . . . A 62 GLN N . 18583 1 + 107 . 1 1 63 63 LYS H H 1 8.49 0.05 . 1 . . . A 63 LYS H . 18583 1 + 108 . 1 1 63 63 LYS N N 15 120.68 0.20 . 1 . . . A 63 LYS N . 18583 1 + 109 . 1 1 64 64 GLU H H 1 9.32 0.05 . 1 . . . A 64 GLU H . 18583 1 + 110 . 1 1 64 64 GLU N N 15 115.09 0.20 . 1 . . . A 64 GLU N . 18583 1 + 111 . 1 1 65 65 SER H H 1 7.70 0.05 . 1 . . . A 65 SER H . 18583 1 + 112 . 1 1 65 65 SER N N 15 115.14 0.20 . 1 . . . A 65 SER N . 18583 1 + 113 . 1 1 66 66 THR H H 1 8.71 0.05 . 1 . . . A 66 THR H . 18583 1 + 114 . 1 1 66 66 THR N N 15 117.81 0.20 . 1 . . . A 66 THR N . 18583 1 + 115 . 1 1 67 67 LEU H H 1 9.34 0.05 . 1 . . . A 67 LEU H . 18583 1 + 116 . 1 1 67 67 LEU N N 15 127.88 0.20 . 1 . . . A 67 LEU N . 18583 1 + 117 . 1 1 68 68 HIS H H 1 8.94 0.05 . 1 . . . A 68 HIS H . 18583 1 + 118 . 1 1 68 68 HIS N N 15 118.71 0.20 . 1 . . . A 68 HIS N . 18583 1 + 119 . 1 1 69 69 LEU H H 1 8.70 0.05 . 1 . . . A 69 LEU H . 18583 1 + 120 . 1 1 69 69 LEU N N 15 124.84 0.20 . 1 . . . A 69 LEU N . 18583 1 + 121 . 1 1 70 70 VAL H H 1 8.70 0.05 . 1 . . . A 70 VAL H . 18583 1 + 122 . 1 1 70 70 VAL N N 15 128.09 0.20 . 1 . . . A 70 VAL N . 18583 1 + 123 . 1 1 71 71 LEU H H 1 8.16 0.05 . 1 . . . A 71 LEU H . 18583 1 + 124 . 1 1 71 71 LEU N N 15 123.45 0.20 . 1 . . . A 71 LEU N . 18583 1 + 125 . 1 1 72 72 ARG H H 1 8.53 0.05 . 1 . . . A 72 ARG H . 18583 1 + 126 . 1 1 72 72 ARG N N 15 122.16 0.20 . 1 . . . A 72 ARG N . 18583 1 + 127 . 1 1 73 73 LEU H H 1 8.53 0.05 . 1 . . . A 73 LEU H . 18583 1 + 128 . 1 1 73 73 LEU N N 15 123.81 0.20 . 1 . . . A 73 LEU N . 18583 1 + 129 . 1 1 74 74 ARG H H 1 8.47 0.05 . 1 . . . A 74 ARG H . 18583 1 + 130 . 1 1 74 74 ARG N N 15 122.07 0.20 . 1 . . . A 74 ARG N . 18583 1 + 131 . 1 1 76 76 GLY H H 1 7.99 0.05 . 1 . . . A 76 GLY H . 18583 1 + 132 . 1 1 76 76 GLY N N 15 115.39 0.20 . 1 . . . A 76 GLY N . 18583 1 + 133 . 2 2 4 4 GLN H H 1 8.260 0.05 . . . . . C 456 GLN H . 18583 1 + 134 . 2 2 4 4 GLN N N 15 123.150 0.3 . . . . . C 456 GLN N . 18583 1 + 135 . 2 2 5 5 LEU H H 1 8.110 0.05 . . . . . C 457 LEU H . 18583 1 + 136 . 2 2 5 5 LEU N N 15 120.050 0.3 . . . . . C 457 LEU N . 18583 1 + 137 . 2 2 6 6 ASN H H 1 8.090 0.05 . . . . . C 458 ASN H . 18583 1 + 138 . 2 2 6 6 ASN N N 15 115.900 0.3 . . . . . C 458 ASN N . 18583 1 + 139 . 2 2 7 7 ALA H H 1 7.840 0.05 . . . . . C 459 ALA H . 18583 1 + 140 . 2 2 7 7 ALA N N 15 122.890 0.3 . . . . . C 459 ALA N . 18583 1 + 141 . 2 2 8 8 MET H H 1 7.990 0.05 . . . . . C 460 MET H . 18583 1 + 142 . 2 2 8 8 MET N N 15 119.210 0.3 . . . . . C 460 MET N . 18583 1 + 143 . 2 2 9 9 ALA H H 1 8.360 0.05 . . . . . C 461 ALA H . 18583 1 + 144 . 2 2 9 9 ALA N N 15 121.420 0.3 . . . . . C 461 ALA N . 18583 1 + 145 . 2 2 10 10 HIS H H 1 8.200 0.05 . . . . . C 462 HIS H . 18583 1 + 146 . 2 2 10 10 HIS N N 15 117.430 0.3 . . . . . C 462 HIS N . 18583 1 + 147 . 2 2 11 11 GLN H H 1 7.840 0.05 . . . . . C 463 GLN H . 18583 1 + 148 . 2 2 11 11 GLN N N 15 118.610 0.3 . . . . . C 463 GLN N . 18583 1 + 149 . 2 2 12 12 ILE H H 1 7.850 0.05 . . . . . C 464 ILE H . 18583 1 + 150 . 2 2 12 12 ILE N N 15 118.710 0.3 . . . . . C 464 ILE N . 18583 1 + 151 . 2 2 13 13 GLN H H 1 8.600 0.05 . . . . . C 465 GLN H . 18583 1 + 152 . 2 2 13 13 GLN N N 15 120.500 0.3 . . . . . C 465 GLN N . 18583 1 + 153 . 2 2 14 14 GLU H H 1 7.450 0.05 . . . . . C 466 GLU H . 18583 1 + 154 . 2 2 14 14 GLU N N 15 115.72 0.3 . . . . . C 466 GLU N . 18583 1 + 155 . 2 2 15 15 MET H H 1 6.800 0.05 . . . . . C 467 MET H . 18583 1 + 156 . 2 2 15 15 MET N N 15 115.080 0.3 . . . . . C 467 MET N . 18583 1 + 157 . 2 2 16 16 PHE H H 1 7.870 0.05 . . . . . C 468 PHE H . 18583 1 + 158 . 2 2 16 16 PHE N N 15 113.750 0.3 . . . . . C 468 PHE N . 18583 1 + 159 . 2 2 18 18 GLN H H 1 9.500 0.05 . . . . . C 470 GLN H . 18583 1 + 160 . 2 2 18 18 GLN N N 15 116.900 0.3 . . . . . C 470 GLN N . 18583 1 + 161 . 2 2 19 19 VAL H H 1 7.7660 0.05 . . . . . C 471 VAL H . 18583 1 + 162 . 2 2 19 19 VAL N N 15 124.44 0.3 . . . . . C 471 VAL N . 18583 1 + 163 . 2 2 21 21 TYR H H 1 8.830 0.05 . . . . . C 473 TYR H . 18583 1 + 164 . 2 2 21 21 TYR N N 15 126.320 0.3 . . . . . C 473 TYR N . 18583 1 + 165 . 2 2 22 22 HIS H H 1 8.680 0.05 . . . . . C 474 HIS H . 18583 1 + 166 . 2 2 22 22 HIS N N 15 113.220 0.3 . . . . . C 474 HIS N . 18583 1 + 167 . 2 2 23 23 LEU H H 1 6.600 0.05 . . . . . C 475 LEU H . 18583 1 + 168 . 2 2 23 23 LEU N N 15 119.450 0.3 . . . . . C 475 LEU N . 18583 1 + 169 . 2 2 24 24 VAL H H 1 7.180 0.05 . . . . . C 476 VAL H . 18583 1 + 170 . 2 2 24 24 VAL N N 15 120.890 0.3 . . . . . C 476 VAL N . 18583 1 + 171 . 2 2 25 25 LEU H H 1 8.100 0.05 . . . . . C 477 LEU H . 18583 1 + 172 . 2 2 25 25 LEU N N 15 118.710 0.3 . . . . . C 477 LEU N . 18583 1 + 173 . 2 2 26 26 GLN H H 1 7.550 0.05 . . . . . C 478 GLN H . 18583 1 + 174 . 2 2 26 26 GLN N N 15 115.520 0.3 . . . . . C 478 GLN N . 18583 1 + 175 . 2 2 27 27 ASP H H 1 7.390 0.05 . . . . . C 479 ASP H . 18583 1 + 176 . 2 2 27 27 ASP N N 15 119.110 0.3 . . . . . C 479 ASP N . 18583 1 + 177 . 2 2 28 28 LEU H H 1 8.400 0.05 . . . . . C 480 LEU H . 18583 1 + 178 . 2 2 28 28 LEU N N 15 118.990 0.3 . . . . . C 480 LEU N . 18583 1 + 179 . 2 2 29 29 GLN H H 1 8.030 0.05 . . . . . C 481 GLN H . 18583 1 + 180 . 2 2 29 29 GLN N N 15 116.850 0.3 . . . . . C 481 GLN N . 18583 1 + 181 . 2 2 30 30 LEU H H 1 7.230 0.05 . . . . . C 482 LEU H . 18583 1 + 182 . 2 2 30 30 LEU N N 15 117.030 0.3 . . . . . C 482 LEU N . 18583 1 + 183 . 2 2 31 31 THR H H 1 8.870 0.05 . . . . . C 483 THR H . 18583 1 + 184 . 2 2 31 31 THR N N 15 110.740 0.3 . . . . . C 483 THR N . 18583 1 + 185 . 2 2 32 32 ARG H H 1 9.030 0.05 . . . . . C 484 ARG H . 18583 1 + 186 . 2 2 32 32 ARG N N 15 117.784 0.3 . . . . . C 484 ARG N . 18583 1 + 187 . 2 2 33 33 SER H H 1 7.971 0.05 . . . . . C 485 SER H . 18583 1 + 188 . 2 2 33 33 SER N N 15 110.880 0.3 . . . . . C 485 SER N . 18583 1 + 189 . 2 2 34 34 VAL H H 1 9.060 0.05 . . . . . C 486 VAL H . 18583 1 + 190 . 2 2 34 34 VAL N N 15 129.980 0.3 . . . . . C 486 VAL N . 18583 1 + 191 . 2 2 35 35 GLU H H 1 9.270 0.05 . . . . . C 487 GLU H . 18583 1 + 192 . 2 2 35 35 GLU N N 15 123.360 0.3 . . . . . C 487 GLU N . 18583 1 + 193 . 2 2 36 36 ILE H H 1 7.980 0.05 . . . . . C 488 ILE H . 18583 1 + 194 . 2 2 36 36 ILE N N 15 119.880 0.3 . . . . . C 488 ILE N . 18583 1 + 195 . 2 2 37 37 THR H H 1 8.250 0.05 . . . . . C 489 THR H . 18583 1 + 196 . 2 2 37 37 THR N N 15 118.020 0.3 . . . . . C 489 THR N . 18583 1 + 197 . 2 2 38 38 THR H H 1 8.350 0.05 . . . . . C 490 THR H . 18583 1 + 198 . 2 2 38 38 THR N N 15 117.400 0.3 . . . . . C 490 THR N . 18583 1 + 199 . 2 2 39 39 ASP H H 1 7.490 0.05 . . . . . C 491 ASP H . 18583 1 + 200 . 2 2 39 39 ASP N N 15 122.260 0.3 . . . . . C 491 ASP N . 18583 1 + 201 . 2 2 40 40 ASN H H 1 8.490 0.05 . . . . . C 492 ASN H . 18583 1 + 202 . 2 2 40 40 ASN N N 15 116.340 0.3 . . . . . C 492 ASN N . 18583 1 + 203 . 2 2 41 41 ILE H H 1 8.000 0.05 . . . . . C 493 ILE H . 18583 1 + 204 . 2 2 41 41 ILE N N 15 121.110 0.3 . . . . . C 493 ILE N . 18583 1 + 205 . 2 2 42 42 LEU H H 1 8.410 0.05 . . . . . C 494 LEU H . 18583 1 + 206 . 2 2 42 42 LEU N N 15 121.930 0.3 . . . . . C 494 LEU N . 18583 1 + 207 . 2 2 43 43 GLU H H 1 8.370 0.05 . . . . . C 495 GLU H . 18583 1 + 208 . 2 2 43 43 GLU N N 15 114.530 0.3 . . . . . C 495 GLU N . 18583 1 + 209 . 2 2 44 44 GLY H H 1 7.630 0.05 . . . . . C 496 GLY H . 18583 1 + 210 . 2 2 44 44 GLY N N 15 107.200 0.3 . . . . . C 496 GLY N . 18583 1 + 211 . 2 2 45 45 ARG H H 1 8.300 0.05 . . . . . C 497 ARG H . 18583 1 + 212 . 2 2 45 45 ARG N N 15 116.830 0.3 . . . . . C 497 ARG N . 18583 1 + 213 . 2 2 46 46 ILE H H 1 7.130 0.05 . . . . . C 498 ILE H . 18583 1 + 214 . 2 2 46 46 ILE N N 15 117.930 0.3 . . . . . C 498 ILE N . 18583 1 + 215 . 2 2 47 47 GLN H H 1 8.340 0.05 . . . . . C 499 GLN H . 18583 1 + 216 . 2 2 47 47 GLN N N 15 125.410 0.3 . . . . . C 499 GLN N . 18583 1 + 217 . 2 2 48 48 VAL H H 1 8.180 0.05 . . . . . C 500 VAL H . 18583 1 + 218 . 2 2 48 48 VAL N N 15 122.810 0.3 . . . . . C 500 VAL N . 18583 1 + 219 . 2 2 50 50 PHE H H 1 8.115 0.05 . . . . . C 502 PHE H . 18583 1 + 220 . 2 2 50 50 PHE N N 15 121.190 0.3 . . . . . C 502 PHE N . 18583 1 + 221 . 2 2 52 52 THR H H 1 7.790 0.05 . . . . . C 504 THR H . 18583 1 + 222 . 2 2 52 52 THR N N 15 119.528 0.3 . . . . . C 504 THR N . 18583 1 + + stop_ + +save_ + diff --git a/tests/data/test_input.toml b/tests/data/test_input.toml index 84499a8..f9ef2bb 100644 --- a/tests/data/test_input.toml +++ b/tests/data/test_input.toml @@ -6,19 +6,11 @@ fractionally_deuterated = true #------------------------------------------------------------------------------------------------ [BMRB] -# BMRB tables as a text file in NMR Star format -# bmrb_table_fname = "/Users/rodrigo/repos/fandas/example/1ubq-bmrb-tables.txt" bmrb_table_fname = "" -# Which should be the first residue number of your sequence. -sequence_start = 1 -# column numbers -resnum_column = 1 -atom_column = 3 -chemical_shift_column = 4 +target_entity = "" #------------------------------------------------------------------------------------------------ [distance] -# distance_fname = "/Users/rodrigo/repos/fandas/example/1ubq-cc-dist.txt" distance_fname = "" distance_cutoff = 3.9 @@ -40,10 +32,10 @@ rev_14n = ["I"] #------------------------------------------------------------------------------------------------ [preset_experiments] selected = [ - "N-H", - "N-(Calpha)-Cx (residues i, i+1 & i-1)", - "N-(Co)-Cx", - "C-C DQ-SQ Correlation", + "N-H", + "N-(Calpha)-Cx (residues i, i+1 & i-1)", + "N-(Co)-Cx", + "C-C DQ-SQ Correlation", ] #------------------------------------------------------------------------------------------------ diff --git a/tests/modules/test_bmrb.py b/tests/modules/test_bmrb.py new file mode 100644 index 0000000..34b36dc --- /dev/null +++ b/tests/modules/test_bmrb.py @@ -0,0 +1,50 @@ +"""Test the BMRB module.""" +import pytest +from pynmrstar.entry import Entry + +from fandas.modules.chemical_shift import BMRB +from fandas.modules.residue import Residue + +from .. import TEST_BMRB_TABLE + + +@pytest.fixture +def bmrb_class(): + """Chemical shift class.""" + + yield BMRB(table_fname=TEST_BMRB_TABLE, entity_id=1) + + +def test__assign(bmrb_class): + bmrb_class._assign() + assert bmrb_class.residues[1].shifts == {} + assert bmrb_class.residues[10].shifts == {"H": 7.82, "N": 109.42} + + +def test_align_to(bmrb_class): + aln_dic = bmrb_class.align_to("EPSDTIENVKAKI") + assert aln_dic == { + 1: 18, + 2: 19, + 3: 20, + 4: 21, + 5: 22, + 6: 23, + 7: 24, + 8: 25, + 9: 26, + 10: 27, + 11: 28, + 12: 29, + 13: 30, + } + + +def test__read(bmrb_class): + entry, residue_dict, seq = bmrb_class._read() + + assert isinstance(entry, Entry) + assert isinstance(residue_dict, dict) + assert isinstance(seq, str) + assert len(residue_dict) == 76 + assert isinstance(residue_dict[1], Residue) diff --git a/tests/modules/test_chemical_shift.py b/tests/modules/test_chemical_shift.py index 8cad984..aa24884 100644 --- a/tests/modules/test_chemical_shift.py +++ b/tests/modules/test_chemical_shift.py @@ -2,9 +2,10 @@ import copy import pytest + from fandas.modules.chemical_shift import ChemShift -from .. import TEST_BMRB_TABLE +# from .. import TEST_BMRB_TABLE @pytest.fixture @@ -12,8 +13,10 @@ def chemshift_class(): """Chemical shift class.""" sequence = "MQIFV" secondary_structure = "naabc" + bmrb_table = "" + bmrb_entity_id = "" - yield ChemShift(sequence, secondary_structure) + yield ChemShift(sequence, secondary_structure, bmrb_table, bmrb_entity_id) def test_assign(chemshift_class): @@ -39,17 +42,6 @@ def test_assign(chemshift_class): assert chemshift_class.residues[1].shifts["C"] == 175.93 -def test_replace_with_bmrb(chemshift_class): - """Test the replace_with_bmrb method.""" - chemshift_class.replace_with_bmrb( - table_fname=TEST_BMRB_TABLE, resnum_col=1, atom_col=3, shift_col=4, seq_offset=1 - ) - - assert chemshift_class.residues[1].shifts["C"] == 170.52 - assert chemshift_class.residues[1].shifts["CA"] == 54.4 - assert chemshift_class.residues[5].shifts["N"] == 128.38 - - @pytest.mark.skip(reason="No way of currently testing this") def test_label(chemshift_class): pass diff --git a/tests/modules/test_experiment.py b/tests/modules/test_experiment.py index f23f8d3..3ebdb68 100644 --- a/tests/modules/test_experiment.py +++ b/tests/modules/test_experiment.py @@ -1,13 +1,15 @@ """Test the experiment module.""" -import pytest -import tempfile import os +import tempfile from pathlib import Path -from fandas.modules.experiment import Experiment + +import pytest + from fandas.modules.chemical_shift import ChemShift +from fandas.modules.experiment import Experiment from fandas.modules.input import InputFile -from .. import TEST_INPUT_FILE, TEST_DISTANCE_FILE +from .. import TEST_DISTANCE_FILE, TEST_INPUT_FILE @pytest.fixture @@ -15,8 +17,10 @@ def chemical_shifts(): """Chemical shift class.""" sequence = "MQIFV" secondary_structure = "naabc" + bmrb_table = "" + bmrb_entity_id = "" - yield ChemShift(sequence, secondary_structure) + yield ChemShift(sequence, secondary_structure, bmrb_table, bmrb_entity_id) @pytest.fixture diff --git a/tests/modules/test_input.py b/tests/modules/test_input.py index b7ec8a4..35890f2 100644 --- a/tests/modules/test_input.py +++ b/tests/modules/test_input.py @@ -1,4 +1,5 @@ import pytest + from fandas.modules.input import InputFile from .. import TEST_INPUT_FILE @@ -24,10 +25,7 @@ def test__load(inputfile_class): }, "BMRB": { "bmrb_table_fname": (""), - "sequence_start": 1, - "resnum_column": 1, - "atom_column": 3, - "chemical_shift_column": 4, + "target_entity": (""), }, "distance": { "distance_fname": "", diff --git a/tests/modules/test_utils.py b/tests/modules/test_utils.py index e9a556b..9c312e4 100644 --- a/tests/modules/test_utils.py +++ b/tests/modules/test_utils.py @@ -1,54 +1 @@ -from fandas.modules.utils import load_bmrbm - -from .. import TEST_BMRB_TABLE - - -def test_load_bmrb(): - """Test the loading of the BMRB table.""" - resnum_col = 1 - atom_col = 3 - shift_col = 4 - observed_dic = load_bmrbm(TEST_BMRB_TABLE, resnum_col, atom_col, shift_col) - expected_dic = { - 1: { - "C": 170.52, - "CA": 54.4, - "CB": 33.4599, - "CE": 17.6847, - "CG": 31.8754, - "H": 8.2666, - "HA": 4.22, - "HB2": 2.07, - "HB3": 2.139, - "HE": 1.8684, - "HG2": 2.4714, - "HG3": 2.2222, - }, - 2: {"N": 116.08}, - 3: { - "C": 175.22, - "CA": 54.6, - "CB": 41.2, - "CD1": 132.3, - "CD2": 131.985, - "CE1": 131.2, - "CE2": 131.0049, - "CG": 139.9524, - "CZ": 129.4, - "H": 8.57, - }, - 4: {"HG1": 0.71, "HG2": 0.76, "N": 120.7885}, - 5: { - "C": 177.3016, - "CA": 54.3, - "CB": 35.5, - "CD": 29.4536, - "CE": 42.0471, - "HG3": 1.4319, - "HZ": 7.5356, - "N": 128.38, - }, - 999: {"N": 128.38}, - } - - assert expected_dic == observed_dic +"""Test the utils.""" From 44728ca4c38c6a754ef2f14fc8edf6d84229db5d Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 17:33:48 +0200 Subject: [PATCH 3/6] bump version --- CHANGELOG.md | 8 +++++++- setup.py | 10 +++++++--- src/fandas/version.py | 2 +- 3 files changed, 15 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index de7c3b3..e83b8ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,12 @@ # CHANGELOG -## v2.2.2 (28/04/2022) - Added missing catalog to the build +## v2.3.0 (01/08/2022) - Add support to BMRB files in NMR-STAR v3 format + +- Only BMRB files in NMR-STAR v3 format are supported. +- If BMRB file is being used, added a feature to automatically align and match the numbering between the input sequence with the sequence observed in the BMRB file. + +* * * +v2.2.2 (28/04/2022) - Added missing catalog to the build * * * v2.2.1 (26/04/2022) - Bugfix when matching numbering from sequence and chemical shift table diff --git a/setup.py b/setup.py index 9e92797..ba57492 100644 --- a/setup.py +++ b/setup.py @@ -1,9 +1,13 @@ -from setuptools import setup, find_packages +from setuptools import find_packages, setup + +with open("requirements.txt") as f: + required = f.read().splitlines() + setup( name="FANDAS", license="Apache License 2.0", - version="2.2.2", + version="2.3.0", author="Siddarth Narasimhan, Rodrigo Honorato", description="Fast Analysis of multidimensional NMR DAta Sets", author_email="", @@ -12,7 +16,7 @@ package_dir={"": "src"}, classifiers=[], python_requires=">=3.6, <4", - install_requires=["numpy", "toml", "pandas"], + install_requires=required, entry_points={ "console_scripts": [ "fandas=fandas.cli:maincli", diff --git a/src/fandas/version.py b/src/fandas/version.py index 37180ed..90f703f 100644 --- a/src/fandas/version.py +++ b/src/fandas/version.py @@ -1,2 +1,2 @@ -VERSION = "2.2.2" +VERSION = "2.3.0" v_major, v_minor, v_patch = VERSION.split(".") From a6fcedf71c5357104cbdcf76c1639a18c553919b Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 17:34:40 +0200 Subject: [PATCH 4/6] Update requirements.txt --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index be21912..0d383d7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,3 +2,4 @@ numpy==1.22.3 pandas==1.4.2 toml==0.10.2 pynmrstar==3.1.0 +biopython==1.79 From e458d296943b9fd3ebb879c9fbe35ee1b8dbf3ff Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 17:49:18 +0200 Subject: [PATCH 5/6] Update cli.py --- src/fandas/cli.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/fandas/cli.py b/src/fandas/cli.py index 4b4ff1e..e3b205f 100644 --- a/src/fandas/cli.py +++ b/src/fandas/cli.py @@ -16,6 +16,7 @@ ) ch.setFormatter(formatter) log.addHandler(ch) +log.propagate = False __author__ = ["Siddarth Narasimhan", "Rodrigo Honorato"] @@ -58,7 +59,7 @@ def maincli(): # Main code def main( input_file, - log_level="DEBUG", + log_level="INFO", ): # Start #=========================================================================# From 65c9eae36abaf27cb1d87ed085e0184cc74d4aa7 Mon Sep 17 00:00:00 2001 From: rodrigo Date: Mon, 1 Aug 2022 17:52:04 +0200 Subject: [PATCH 6/6] linting --- CHANGELOG.md | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e83b8ff..90020ce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,15 +5,18 @@ - Only BMRB files in NMR-STAR v3 format are supported. - If BMRB file is being used, added a feature to automatically align and match the numbering between the input sequence with the sequence observed in the BMRB file. -* * * +--- + v2.2.2 (28/04/2022) - Added missing catalog to the build -* * * +--- + v2.2.1 (26/04/2022) - Bugfix when matching numbering from sequence and chemical shift table - The matching between the chemical shift data and the sequence numbering was not being done correctly, should not be fixed. -* * * +--- + v2.2.0 (20/04/2022) - Complete code redesign - Most of the code has been completely redesigned, to make the code more clear, testable and extensible @@ -22,19 +25,23 @@ v2.2.0 (20/04/2022) - Complete code redesign - Previous experiments are now "presets" in the catalog - Added unittests, coverage report and linting check with github actions -*Developer note: The changes to the code would be worth of a **major** version (v3.0.0) since the API was completely redesigned but in this project it makes more sense for the major version to be incremented when relevant new **scientific** features are added.* +_Developer note: The changes to the code would be worth of a **major** version (v3.0.0) since the API was completely redesigned but in this project it makes more sense for the major version to be incremented when relevant new **scientific** features are added._ + +--- -* * * v2.1.0 (14/02/2022) - Implemented the `offset` feature - The matching of the numbering between the BMRB table and the sequence was previously done by the server. - Reformat standard table to a more human-readable format - added `pandas` dependency -* * * +--- + v2.0.3 (12/02/2022) - Fixed bug with indexes in `replace_bmrb` -* * * +--- + v2.0.2 (08/02/2022) - Fixed bug caused by refactoring that caused rev_label function to not recieve the correct arguments -* * * +--- + v2.0.1 (01/02/2022) - Fixed bugs with DQ and distance related experiments