› 3tgd

X-ray diffraction
1.8Å resolution

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

Released:
DOI: 10.2210/pdb3tgd/pdb
PDB entry 3tgd coloured by chain, front view.
PDB entry 3tgd coloured by chain, side view.
PDB entry 3tgd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Page RC, Amick J, Misra S

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 analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158730 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-conjugating enzyme E2 D2 Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 17.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 49.342Å b: 50.277Å c: 64.299Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.203
Expression system: Escherichia coli

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