› 2clw

X-ray diffraction
1.94Å resolution

Crystal structure of human ubiquitin-conjugating enzyme UbcH5B

Released:
DOI: 10.2210/pdb2clw/pdb
PDB entry 2clw coloured by chain, front view.
PDB entry 2clw coloured by chain, side view.
PDB entry 2clw coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dodd RB, Read RJ

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158730 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 18.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin-conjugating enzyme E2 D2 Chains: B, C, D
Molecule details ›
Chains: B, C, D
Length: 165 amino acids
Theoretical weight: 18.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand GOL 3 x GOL
1 modified residue:
Ligand CME 1 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.2
Spacegroup: P21
Unit cell:
a: 45.585Å b: 65.803Å c: 101.677Å
α: 90° β: 89.96° γ: 90°
R-values:
R R work R free
0.218 0.218 0.255
Expression system: Escherichia coli BL21(DE3)

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