3IHP | pdb_00003ihp

Covalent Ubiquitin-Usp5 Complex

• PDB DOI: https://doi.org/10.2210/pdb3IHP/pdb

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


• Deposited: 2009-07-30 Released: 2009-12-29 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Models: experimental

Literature

Covalent Ubiquitin-Usp5 Complex

Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Weigelt, J., Bountra, C., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 208.2 kDa 
• Atom Count: 11,800 
• Modeled Residue Count: 1,504 
• Deposited Residue Count: 1,858 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 5	A, B	854	Homo sapiens	Mutation(s): 0  Gene Names: ISOT, USP5 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P45974 (Homo sapiens) Explore P45974  Go to UniProtKB:  P45974
PHAROS:  P45974 GTEx:  ENSG00000111667

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D	75	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2
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
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NEH	G [auth C], H [auth D]	ETHANAMINE C2 H7 N QUSNBJAOOMFDIB-UHFFFAOYSA-N
CL	I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.295	α = 90
b = 188.845	β = 90
c = 207.86	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: 2009-12-29 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-12-29
  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