› 2yu1

X-ray diffraction
2.7Å resolution

Crystal structure of hJHDM1A complexed with a-ketoglutarate

Released:
DOI: 10.2210/pdb2yu1/pdb
PDB entry 2yu1 coloured by chain, front view.
PDB entry 2yu1 coloured by chain, side view.
PDB entry 2yu1 coloured by chain, top view.
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
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 Chain: A
Molecule details ›
Chain: A
Length: 451 amino acids
Theoretical weight: 52.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9Y2K7 (Residues: 1-517; Coverage: 39%)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Sequence domains: Jumonji helical domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand FE2 1 x FE2
Ligand AKG 1 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P3121
Unit cell:
a: 81.255Å b: 81.255Å c: 124.01Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.238 0.238 0.273
Expression system: Escherichia coli BL21

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