2IBI

Covalent Ubiquitin-USP2 Complex

• PDB DOI: https://doi.org/10.2210/pdb2IBI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-09-11 Released: 2006-10-24 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Bernstein, G., Xue, S., Finerty Jr., P.J., MacKenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.190 
• R-Value Observed: 0.194 

Starting Models: experimental

Literature

Covalent Ubiquitin-USP2 Complex

Avvakumov, G.V., Walker, J.R., Bernstein, G., Xue, S., Finerty Jr., P.J., MacKenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

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: 51.34 kDa 
• Atom Count: 3,422 
• Modelled Residue Count: 410 
• Deposited Residue Count: 449 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 2	A	374	Homo sapiens	Mutation(s): 2  Gene Names: USP2, UBP41 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	75	Homo sapiens	Mutation(s): 0  Gene Names: Rps27a, UBA52, UBB, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NEH	D [auth B]	ETHANAMINE C2 H7 N QUSNBJAOOMFDIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.190 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.839	α = 90
b = 54.4	β = 107.66
c = 75.021	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Bernstein, G., Xue, S., Finerty Jr., P.J., MacKenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description