› 6afg

X-ray diffraction
1.5Å resolution

DJ-1 with compound 9

Released:
DOI: 10.2210/pdb6afg/pdb
PDB entry 6afg coloured by chain, front view.
PDB entry 6afg coloured by chain, side view.
PDB entry 6afg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K
ACS Chem Biol 13 2783-2793 (2018)
PMID: 30063823

Function and Biology Details

Reaction catalysed: 
An N(6)-(1-hydroxy-2-oxopropyl)-[protein]-L-lysine + H(2)O = a [protein]-L-lysine + lactate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189207 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Parkinson disease protein 7 Chain: A
Molecule details ›
Chain: A
Length: 189 amino acids
Theoretical weight: 19.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q99497 (Residues: 1-189; Coverage: 100%)
Gene name: PARK7
Sequence domains: DJ-1/PfpI family
Structure domains: Rossmann fold

Ligands and Environments

1 bound ligand:
Ligand 72V 2 x 72V
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P3121
Unit cell:
a: 75.45Å b: 75.45Å c: 75.64Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.118 0.116 0.148
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

Small Substrate or Large? Debate Over the Mechanism of Glycation Adduct Repair by DJ-1.
Jun et al. (2020)
4 more

1 mention without citation

Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs.
Tikhonov et al. (2021)