› 4bbq

X-ray diffraction
2.24Å resolution

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

Released:
DOI: 10.2210/pdb4bbq/pdb
PDB entry 4bbq coloured by chain, front view.
PDB entry 4bbq coloured by chain, side view.
PDB entry 4bbq coloured by chain, top view.
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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195143 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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)
UniProt:
  • Canonical: Q9Y2K7 (Residues: 567-681; Coverage: 10%)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

2 bound ligands:
Ligand EDO 1 x EDO
Ligand ZN 8 x ZN
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-values:
R R work R free
0.198 0.197 0.221
Expression system: Escherichia coli BL21(DE3)

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