Download MendeleyStructure of USP7 with a novel viral protein
Chavoshi, S., Egorova, O., Lacdao, I.K., Farhadi, S., Sheng, Y., Saridakis, V.(2016) J Biological Chem
4YSI | pdb_00004ysi
Structure of USP7 with a novel viral protein
- PDB DOI: https://doi.org/10.2210/pdb4YSI/pdb
- Classification: HYDROLASE/Peptide
- Organism(s): Homo sapiens, Human gammaherpesvirus 8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-03-17 Released: 2016-02-03
- Funding Organization(s): Canadian Institutes of Health Research (CIHR)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.02 Å
- R-Value Free: 0.160 (Depositor), 0.160 (DCC)
- R-Value Work: 0.154 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.154 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin carboxyl-terminal hydrolase 7 | 143 | Homo sapiens | Mutation(s): 0 Gene Names: USP7, HAUSP EC: 3.4.19.12 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q93009 (Homo sapiens) Explore Q93009 Go to UniProtKB: Q93009 | |||||
PHAROS: Q93009 GTEx: ENSG00000187555 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q93009 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SER-PRO-GLY-GLU-GLY-PRO-SER-GLY | 8 | Human gammaherpesvirus 8 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for F5HF68 (Human herpesvirus 8 type P (isolate GK18)) Explore F5HF68 Go to UniProtKB: F5HF68 | |||||
Entity Groups | |||||
| UniProt Group | F5HF68 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.02 Å
- R-Value Free: 0.160 (Depositor), 0.160 (DCC)
- R-Value Work: 0.154 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.154 (Depositor)
Space Group: P 41
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.975 | α = 90 |
| b = 69.975 | β = 90 |
| c = 45.444 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| RESOLVE | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-02-03 Deposition Author(s): Chavoshi, S., Saridakis, V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Canadian Institutes of Health Research (CIHR) | Canada | 106583 |
Revision History (Full details and data files)
- Version 1.0: 2016-02-03
Type: Initial release - Version 1.1: 2017-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2017-09-27
Changes: Author supporting evidence - Version 1.3: 2020-01-08
Changes: Author supporting evidence - Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description
