2CLW | pdb_00002clw

Crystal structure of human ubiquitin-conjugating enzyme UbcH5B

• PDB DOI: https://doi.org/10.2210/pdb2CLW/pdb
• Entry: 2CLW supersedes: 2C4O

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


• Deposited: 2006-05-02 Released: 2007-06-12 
• Deposition Author(s): Dodd, R.B., Read, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (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 PISA (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.76 kDa 
• Atom Count: 5,091 
• Modeled Residue Count: 600 
• Deposited Residue Count: 660 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 D2	A	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 P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 D2	B, C, D	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 P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.95 Å
• R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.585	α = 90
b = 65.803	β = 89.96
c = 101.677	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: 2007-06-12 
Deposition Author(s): Dodd, R.B., Read, R.J.
• This entry supersedes: 2C4O

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2014-08-13
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary