+Open data
-Basic information
Entry | Database: PDB / ID: 6vn4 | ||||||
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Title | USP7 IN COMPLEX WITH LIGAND COMPOUND 1 | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 7 | ||||||
Keywords | HYDROLASE / USP7 / DUB / DEUBIQUITINASE | ||||||
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 / 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: 2.69 Å | ||||||
Authors | Leger, P.R. / Wustrow, D.J. / Hu, D.X. / Krapp, S. / Maskos, K. / Blaesse, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity. Authors: Leger, P.R. / Hu, D.X. / Biannic, B. / Bui, M. / Han, X. / Karbarz, E. / Maung, J. / Okano, A. / Osipov, M. / Shibuya, G.M. / Young, K. / Higgs, C. / Abraham, B. / Bradford, D. / Cho, C. / ...Authors: Leger, P.R. / Hu, D.X. / Biannic, B. / Bui, M. / Han, X. / Karbarz, E. / Maung, J. / Okano, A. / Osipov, M. / Shibuya, G.M. / Young, K. / Higgs, C. / Abraham, B. / Bradford, D. / Cho, C. / Colas, C. / Jacobson, S. / Ohol, Y.M. / Pookot, D. / Rana, P. / Sanchez, J. / Shah, N. / Sun, M. / Wong, S. / Brockstedt, D.G. / Kassner, P.D. / Schwarz, J.B. / Wustrow, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vn4.cif.gz | 297.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vn4.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/6vn4 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/6vn4 | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 40475.738 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 / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→78.41 Å / Num. obs: 21844 / % possible obs: 94.4 % / Redundancy: 3 % / Biso Wilson estimate: 75.078 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.045 / Χ2: 1.087 / Net I/σ(I): 12.86 |
Reflection shell | Resolution: 2.69→2.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 87 / CC1/2: 0.937 / Rrim(I) all: 0.55 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: In House Model Resolution: 2.69→44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 42.614 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 Details: U VALUES : WITH TLS ADDED 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 max: 288.66 Å2 / Biso mean: 79.728 Å2 / Biso min: 38.73 Å2
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Refinement step | Cycle: final / Resolution: 2.69→44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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