› 6gdy

X-ray diffraction
2.04Å resolution

Crystal structure of 2OG oxygenase JMJD6 (aa 1-343) in complex with Fe(II) and 2OG

Released:
DOI: 10.2210/pdb6gdy/pdb
PDB entry 6gdy coloured by chain, front view.
PDB entry 6gdy coloured by chain, side view.
PDB entry 6gdy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6.
Islam MS, McDonough MA, Chowdhury R, Gault J, Khan A, Pires E, Schofield CJ
J Biol Chem 294 11637-11652 (2019)
PMID: 31147442

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180087 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 40.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6NYC1 (Residues: 1-343; Coverage: 85%)
Gene names: JMJD6, KIAA0585, PSR, PTDSR
Sequence domains: JmjC domain, hydroxylase
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand FE 2 x FE
Ligand AKG 2 x AKG
Ligand NA 1 x NA
Ligand PO4 10 x PO4
Ligand EPE 2 x EPE
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 47.15Å b: 96.99Å c: 93.76Å
α: 90° β: 95.84° γ: 90°
R-values:
R R work R free
0.181 0.18 0.216
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Protein arginine methylation: from enigmatic functions to therapeutic targeting.
Wu et al. (2021)
6 more

4 mentions without citation

Inhibition of JMJD6 by 2-Oxoglutarate Mimics.
Islam et al. (2022)
3 more