7XHK

High-resolution X-ray cocrystal structure of USP7 in complex with LX04-46

PDB DOI: https://doi.org/10.2210/pdb7XHK/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-08 Released: 2023-06-14
Deposition Author(s): Sun, H.B., Wen, X.A.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

High-resolution X-ray cocrystal structure of USP7 in complex with LX04-46

Wen, X.A.

To be published.

Macromolecule Content

Total Structure Weight: 40.86 kDa
Atom Count: 2,674
Modelled Residue Count: 334
Deposited Residue Count: 348
Unique protein chains: 1

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	A [auth B]	348	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DVU Query on DVU Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B	B	~{N}-[[4-[6-[[1-[[2-chloranyl-4-(furan-2-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-3-yl]phenyl]methyl]methanamide C₃₁ H₃₁ Cl N₆ O₄ NBSWPCOVWWWQAK-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264
R-Value Work: 0.220
R-Value Observed: 0.222
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.961	α = 90
b = 70.856	β = 95.36
c = 77.584	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81773584, 91853125

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.