5xit

X-ray diffraction
2.25Å resolution

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

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-158828 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: D, F
Molecule details ›
Chains: D, F
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62983 (Residues: 1-76; Coverage: 49%)
Gene names: Rps27a, Uba80, Ubcep1
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase RNF168 Chains: A, E
Molecule details ›
Chains: A, E
Length: 81 amino acids
Theoretical weight: 9.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IYW5 (Residues: 113-188; Coverage: 13%)
Gene name: RNF168
Ubiquitin Chains: B, H
Molecule details ›
Chains: B, H
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62983 (Residues: 1-76; Coverage: 49%)
Gene names: Rps27a, Uba80, Ubcep1
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P1
Unit cell:
a: 45.372Å b: 50.019Å c: 64.407Å
α: 73.49° β: 69.69° γ: 73.82°
R-values:
R R work R free
0.221 0.22 0.239
Expression system: Escherichia coli