3TGD

Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b

• PDB DOI: https://doi.org/10.2210/pdb3TGD/pdb

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


• Deposited: 2011-08-17 Released: 2011-08-31 
• Deposition Author(s): Page, R.C., Amick, J., Misra, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b

Page, R.C., Amick, J., Misra, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 17.16 kDa 
• Atom Count: 1,456 
• Modelled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A	152	Homo sapiens	Mutation(s): 0  Gene Names: UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.342	α = 90
b = 50.277	β = 90
c = 64.299	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Page, R.C., Amick, J., Misra, S.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description