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Yorodumi- PDB-5nge: Crystal structure of USP7 in complex with the non-covalent inhibi... -
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-Basic information
Entry | Database: PDB / ID: 5nge | ||||||
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Title | Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671 | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 7 | ||||||
Keywords | HYDROLASE / DEUBIQUITINATION | ||||||
Function / homology | Function and homology information regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / protein ubiquitination / Ub-specific processing proteases / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Turnbull, A.P. / Krajewski, W.W. / Ioannidis, S. / Kessler, B.M. / Komander, D. | ||||||
Citation | Journal: Nature / Year: 2017 Title: Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Authors: Turnbull, A.P. / Ioannidis, S. / Krajewski, W.W. / Pinto-Fernandez, A. / Heride, C. / Martin, A.C.L. / Tonkin, L.M. / Townsend, E.C. / Buker, S.M. / Lancia, D.R. / Caravella, J.A. / Toms, A. ...Authors: Turnbull, A.P. / Ioannidis, S. / Krajewski, W.W. / Pinto-Fernandez, A. / Heride, C. / Martin, A.C.L. / Tonkin, L.M. / Townsend, E.C. / Buker, S.M. / Lancia, D.R. / Caravella, J.A. / Toms, A.V. / Charlton, T.M. / Lahdenranta, J. / Wilker, E. / Follows, B.C. / Evans, N.J. / Stead, L. / Alli, C. / Zarayskiy, V.V. / Talbot, A.C. / Buckmelter, A.J. / Wang, M. / McKinnon, C.L. / Saab, F. / McGouran, J.F. / Century, H. / Gersch, M. / Pittman, M.S. / Marshall, C.G. / Raynham, T.M. / Simcox, M. / Stewart, L.M.D. / McLoughlin, S.B. / Escobedo, J.A. / Bair, K.W. / Dinsmore, C.J. / Hammonds, T.R. / Kim, S. / Urbe, S. / Clague, M.J. / Kessler, B.M. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nge.cif.gz | 270.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nge.ent.gz | 219.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5nge ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5nge | HTTPS FTP |
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-Related structure data
Related structure data | 5ngfC 1nb8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 212 - 554 / Label seq-ID: 7 - 349
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-Components
#1: Protein | Mass: 41148.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% (w/v) polyethylene glycol (PEG) 1500, 100 mM MMT pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→77.95 Å / Num. obs: 31221 / % possible obs: 96.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.719 / Num. measured obs: 5256 / Num. unique all: 1564 / CC1/2: 0.588 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NB8 Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 19.066 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.274 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.541 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→50 Å
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Refine LS restraints |
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