2C4P | pdb_00002c4p

Crystal structure of human ubiquitin-conjugating enzyme UbcH5A

• PDB DOI: https://doi.org/10.2210/pdb2C4P/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-21 Released: 2006-11-22 
• Deposition Author(s): Dodd, R.B., Read, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structures of Two Human Ubiquitin-Conjugating Enzymes from Twinned Crystals

Dodd, R.B., Read, R.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 37.39 kDa 
• Atom Count: 2,458 
• Modeled Residue Count: 299 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 D1	A, B	165	Homo sapiens	Mutation(s): 0  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 P51668 (Homo sapiens) Explore P51668  Go to UniProtKB:  P51668
PHAROS:  P51668 GTEx:  ENSG00000072401

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.621	α = 90
b = 50.565	β = 90
c = 66.043	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-22 
Deposition Author(s): Dodd, R.B., Read, R.J.

Revision History  

• Version 1.0: 2006-11-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description