› 8ik6

X-ray diffraction
3.3Å resolution

pUbl depleted Parkin complex with pUbiquitin

Released:
DOI: 10.2210/pdb8ik6/pdb
PDB entry 8ik6 coloured by chain, front view.
PDB entry 8ik6 coloured by chain, side view.
PDB entry 8ik6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans.
Lenka DR, Dahe SV, Antico O, Sahoo P, Prescott AR, Muqit MMK, Kumar A
Elife 13 (2024)
PMID: 39221915

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-271767 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase parkin Chains: A, C
Molecule details ›
Chains: A, C
Length: 327 amino acids
Theoretical weight: 36.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60260 (Residues: 139-465; Coverage: 70%)
Gene names: PARK2, PRKN
Sequence domains:
Ubiquitin Chains: B, D
Molecule details ›
Chains: B, D
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

Ligands and Environments

2 bound ligands:
Ligand ZN 14 x ZN
Ligand SO4 9 x SO4
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P6422
Unit cell:
a: 187.805Å b: 187.805Å c: 141.857Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.234 0.27
Expression system: Escherichia coli BL21(DE3)

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