3NHE | pdb_00003nhe

High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb3NHE/pdb

• Classification: Hydrolase/protein binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-14 Released: 2010-06-30 
• Deposition Author(s): Schormann, N., DeLucas, L.J., Powell McCombs, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Models: experimental

Literature

High resolution structure of USP2a in complex with ubiquitin

Schormann, N., Powell McCombs, D., DeLucas, L.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.86 kDa 
• Atom Count: 3,950 
• Modelled Residue Count: 414 
• Deposited Residue Count: 424 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 2	A	348	Homo sapiens	Mutation(s): 0  Gene Names: UBP41, USP2 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
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	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA52, UBB, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
PHAROS:  P62979 GTEx:  ENSG00000143947

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.771	α = 90
b = 53.961	β = 107.71
c = 74.719	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Schormann, N., DeLucas, L.J., Powell McCombs, D.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary