› 5ulf

X-ray diffraction
1.8Å resolution

Crystal Structure of a UbcH5b~Ub conjugate

Released:
DOI: 10.2210/pdb5ulf/pdb
PDB entry 5ulf coloured by chain, front view.
PDB entry 5ulf coloured by chain, side view.
PDB entry 5ulf coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Middleton AJ, Day CL, Wright JD

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143258 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 152 amino acids
Theoretical weight: 17.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: B, D
Molecule details ›
Chains: B, D
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P1
Unit cell:
a: 29.336Å b: 61.356Å c: 62.824Å
α: 102.84° β: 91.66° γ: 90.02°
R-values:
R R work R free
0.229 0.227 0.261
Expression system: Escherichia coli BL21

Quick links