X-ray diffraction
2.7Å resolution

Crystal structure of hJHDM1A without a-ketoglutarate

Source organism: Homo sapiens
Entry author: Han Z

Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Lysine-specific demethylase 2A Chain: A
Molecule details ›
Chain: A
Length: 451 amino acids
Theoretical weight: 52.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
  • Canonical: Q9Y2K7 (Residues: 1-517; Coverage: 39%)
  • Best match: Q9Y2K7-5 (Residues: 54-78)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Sequence domains: Jumonji helical domain
Structure domains:

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P3121
Unit cell:
a: 81.15Å b: 81.15Å c: 124.47Å
α: 90° β: 90° γ: 120°
R R work R free
0.248 0.248 0.287
Expression system: Escherichia coli BL21