X-ray diffraction
2.24Å resolution

Crystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11)

Source organism: Homo sapiens
Entry authors: Allerston CK, Watson AA, Edlich C, Li B, Chen Y, Ball L, Krojer T, Arrowsmith CH, Edwards A, Bountra C, von Delft F, Laue ED, Gileadi O

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:
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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 117 amino acids
Theoretical weight: 13.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
  • Canonical: Q9Y2K7 (Residues: 567-681; Coverage: 10%)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 49.024Å b: 30.053Å c: 90.824Å
α: 90° β: 91.66° γ: 90°
R R work R free
0.198 0.197 0.221
Expression system: Escherichia coli BL21(DE3)