3V6C | pdb_00003v6c

Crystal Structure of USP2 in complex with mutated ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb3V6C/pdb

• Classification: hydrolase/signaling protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-12-19 Released: 2012-12-19 
• Deposition Author(s): Neculai, M., Ernst, A., Sidhu, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of USP2 in complex with mutated ubiquitin

Neculai, M., Ernst, A., Sidhu, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.73 kDa 
• Atom Count: 3,818 
• Modeled Residue Count: 408 
• Deposited Residue Count: 458 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 2	A	367	Homo sapiens	Mutation(s): 0  Gene Names: UBP41, usp02.258.605, USP2 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O75604 (Homo sapiens) Explore O75604  Go to UniProtKB:  O75604
PHAROS:  O75604 GTEx:  ENSG00000036672

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	91	Homo sapiens	Mutation(s): 4  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.735	α = 90
b = 84.077	β = 90
c = 86.915	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Neculai, M., Ernst, A., Sidhu, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description