2w2i

X-ray diffraction
2.1Å resolution

Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

Released:

Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-109719 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4E Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 358 amino acids
Theoretical weight: 41.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B2RXH2 (Residues: 1-336; Coverage: 66%)
Gene names: KDM4DL, KDM4E
Sequence domains:
Structure domains: Cupin

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: I222
Unit cell:
a: 90.904Å b: 111.009Å c: 224.199Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.236
Expression system: Escherichia coli BL21(DE3)