7XHH | pdb_00007xhh

High-resolution X-ray cocrystal structure of USP7 in complex with X4

PDB DOI: https://doi.org/10.2210/pdb7XHH/pdb

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

Deposited: 2022-04-08 Released: 2023-04-19
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: 2.10 Å
R-Value Free:
0.218 (Depositor), 0.201 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 X4

Wen, X.A.

To be published.

Macromolecule Content

Total Structure Weight: 81.65 kDa
Atom Count: 5,788
Modeled Residue Count: 686
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	A, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DYO (Subject of Investigation/LOI) Query on DYO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	3-[4-(aminomethyl)phenyl]-6-[[1-[[2-chloranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-pyrazolo[4,3-d]pyrimidin-7-one C₂₈ H₂₉ Cl N₈ O₃ SUBLUDSEMODLLX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.218 (Depositor), 0.201 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.034	α = 90
b = 68.904	β = 100.32
c = 81.788	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

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: 2023-04-19
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.