› 8ikm

X-ray diffraction
1.92Å resolution

Function and Biology Details

Reaction catalysed: 
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-251271 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase parkin Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 27.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60260 (Residues: 141-382; Coverage: 52%)
Gene names: PARK2, PRKN
Sequence domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 75 amino acids
Theoretical weight: 8.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62987 (Residues: 1-75; Coverage: 59%)
Gene names: UBA52, UBCEP2
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase parkin Chain: C
Molecule details ›
Chain: C
Length: 146 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60260 (Residues: 1-140; Coverage: 30%)
  • Best match: O60260-6 (Residues: 1-57)
Gene names: PARK2, PRKN
Sequence domains: Ubiquitin family

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand GOL 1 x GOL
Ligand PEG 1 x PEG
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P3221
Unit cell:
a: 83.804Å b: 83.804Å c: 105.033Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.205 0.232
Expression system: Escherichia coli BL21(DE3)

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