› 1x23

X-ray diffraction
1.85Å resolution

Crystal structure of ubch5c

Released:
DOI: 10.2210/pdb1x23/pdb
PDB entry 1x23 coloured by chain, front view.
PDB entry 1x23 coloured by chain, side view.
PDB entry 1x23 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Nakanishi M, Teshima N, Mizushima T, Murata S, Tanaka K, Yamane T

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-158193 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-conjugating enzyme E2 D3 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 155 amino acids
Theoretical weight: 17.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 1-147; Coverage: 100%)
Gene names: UBC5C, UBCH5C, UBE2D3
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: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 61.998Å b: 44.334Å c: 97.584Å
α: 90° β: 93.36° γ: 90°
R-values:
R R work R free
0.204 0.199 0.282
Expression system: Escherichia coli

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