› 7yxl

X-ray diffraction
2.2Å resolution

Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and N-oxalyl-D-phenylalanine (NOFD)

Released:
DOI: 10.2210/pdb7yxl/pdb
PDB entry 7yxl coloured by chain, front view.
PDB entry 7yxl coloured by chain, side view.
PDB entry 7yxl coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans.
Chowdhury R, Abboud MI, Wiley J, Tumber A, Markolovic S, Schofield CJ
Sci Rep 12 6065 (2022)
PMID: 35410347

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194305 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
JmjC domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 322 amino acids
Theoretical weight: 36.71 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9VU77 (Residues: 1-316; Coverage: 100%)
Gene names: CG10133, Dmel\CG10133, Dmel_CG10133, JMJD7
Sequence domains: Cupin-like domain

Ligands and Environments

5 bound ligands:
Ligand MN 2 x MN
Ligand MG 2 x MG
Ligand NDF 2 x NDF
Ligand EDO 7 x EDO
Ligand ACT 2 x ACT
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 55.02Å b: 65.16Å c: 99.22Å
α: 90° β: 100.77° γ: 90°
R-values:
R R work R free
0.191 0.188 0.23
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Recent Advances and Therapeutic Implications of 2-Oxoglutarate-Dependent Dioxygenases in Ischemic Stroke.
Xie et al. (2023)
1 other article