7XHH

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

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

Wen, X.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DYO (Subject of Investigation/LOI)	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Sun, H.B., Wen, X.A.

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

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description