5ydk

X-ray diffraction
2.5Å resolution

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form

Released:

Function and Biology Details

Reaction catalysed:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-158823 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase RNF168 Chains: A, F, G, L
Molecule details ›
Chains: A, F, G, L
Length: 87 amino acids
Theoretical weight: 10.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IYW5 (Residues: 113-194; Coverage: 14%)
Gene name: RNF168
Ubiquitin Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62979 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family
Ubiquitin Chains: C, D, I, J
Molecule details ›
Chains: C, D, I, J
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62979 (Residues: 1-77; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 85.344Å b: 64.12Å c: 117.464Å
α: 90° β: 109.62° γ: 90°
R-values:
R R work R free
0.231 0.23 0.26
Expression system: Escherichia coli