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Yorodumi- PDB-5uqx: USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uqx | ||||||
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Title | USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl-[3,3'-bipyridine]-6-carboxamide) | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 7 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HAUSP / USP7 / SBDD / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / K48-linked deubiquitinase activity / protein deubiquitination / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation ...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 / K48-linked deubiquitinase activity / protein deubiquitination / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / negative regulation of gluconeogenesis / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / p53 binding / rhythmic process / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / 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: 2.23 Å | ||||||
Authors | Murray, J.M. / Rouge, L. | ||||||
Citation | Journal: Nature / Year: 2017 Title: USP7 small-molecule inhibitors interfere with ubiquitin binding. Authors: Kategaya, L. / Di Lello, P. / Rouge, L. / Pastor, R. / Clark, K.R. / Drummond, J. / Kleinheinz, T. / Lin, E. / Upton, J.P. / Prakash, S. / Heideker, J. / McCleland, M. / Ritorto, M.S. / ...Authors: Kategaya, L. / Di Lello, P. / Rouge, L. / Pastor, R. / Clark, K.R. / Drummond, J. / Kleinheinz, T. / Lin, E. / Upton, J.P. / Prakash, S. / Heideker, J. / McCleland, M. / Ritorto, M.S. / Alessi, D.R. / Trost, M. / Bainbridge, T.W. / Kwok, M.C.M. / Ma, T.P. / Stiffler, Z. / Brasher, B. / Tang, Y. / Jaishankar, P. / Hearn, B.R. / Renslo, A.R. / Arkin, M.R. / Cohen, F. / Yu, K. / Peale, F. / Gnad, F. / Chang, M.T. / Klijn, C. / Blackwood, E. / Martin, S.E. / Forrest, W.F. / Ernst, J.A. / Ndubaku, C. / Wang, X. / Beresini, M.H. / Tsui, V. / Schwerdtfeger, C. / Blake, R.A. / Murray, J. / Maurer, T. / Wertz, I.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uqx.cif.gz | 295.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uqx.ent.gz | 238.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/5uqx ftp://data.pdbj.org/pub/pdb/validation_reports/uq/5uqx | HTTPS FTP |
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-Related structure data
Related structure data | 5uqvC 1nb8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42634.148 Da / Num. of mol.: 2 / Fragment: UNP residues 192-539 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 1000, 0.1M Tris-HCl 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.23→38.145 Å / Num. obs: 37714 / % possible obs: 96.8 % / Redundancy: 3.8 % / CC1/2: 0.595 / Rpim(I) all: 0.113 / Rrim(I) all: 0.211 / Net I/σ(I): 9.1 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NB8 Resolution: 2.23→38.145 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.9 Å2 / Biso mean: 53.678 Å2 / Biso min: 20.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→38.145 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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