[English] 日本語

- PDB-5kye: Crystal structure of USP7 catalytic domain [H294E] mutant in comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kye | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin | ||||||
![]() |
| ||||||
![]() | HYDROLASE / USP7 catalytic domain / deubiquitinase / H294E mutant / ubiquitin | ||||||
Function / homology | ![]() regulation of telomere capping / regulation of establishment of protein localization to telomere / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont-mediated disruption of host cell PML body ...regulation of telomere capping / regulation of establishment of protein localization to telomere / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / symbiont entry into host cell via disruption of host cell envelope / negative regulation of gene expression via chromosomal CpG island methylation / virus tail / protein deubiquitination / negative regulation of gluconeogenesis / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / regulation of circadian rhythm / PML body / regulation of protein stability / 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 / Ub-specific processing proteases / protein ubiquitination / protein stabilization / nuclear body / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rouge, L. / Ozen, A. | ||||||
![]() | ![]() Title: Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation. Authors: Ozen, A. / Rouge, L. / Bashore, C. / Hearn, B.R. / Skelton, N.J. / Dueber, E.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 146.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kybC ![]() 5kycC ![]() 5kydC ![]() 5kyfC ![]() 1nbfS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40578.848 Da / Num. of mol.: 2 / Fragment: UNP residues 192-538 / Mutation: H294E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.97→53.892 Å / Num. obs: 57873 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 29.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4 | ||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1NBF Resolution: 1.97→53.892 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 206.73 Å2 / Biso mean: 39.2332 Å2 / Biso min: 17.19 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→53.892 Å
|