PDBe 6glc

X-ray diffraction
1.8Å resolution

Structure of phospho-Parkin bound to phospho-ubiquitin

Released:
Source organism: Homo sapiens
Primary publication:
Mechanism of parkin activation by PINK1.
Nature (2018)
PMID: 29995846

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 dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase parkin Chain: A
Molecule details ›
Chain: A
Length: 389 amino acids
Theoretical weight: 43.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60260 (Residues: 1-382; Coverage: 82%)
Gene names: PARK2, PRKN
Sequence domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments


1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P3221
Unit cell:
a: 83.931Å b: 83.931Å c: 105.119Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.18 0.205
Expression system: Escherichia coli