› 5fyi

X-ray diffraction
2.1Å resolution

Crystal structure of human JMJD2A in complex with pyruvate

Released:
DOI: 10.2210/pdb5fyi/pdb
PDB entry 5fyi coloured by chain, front view.
PDB entry 5fyi coloured by chain, side view.
PDB entry 5fyi coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Nowak R, Kopec J, Johansson C, Szykowska A, von Delft F, Arrowsmith CH, Bountra C, Edwards A, Oppermann U

Function and Biology Details

Reactions 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)
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-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-130863 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4A Chains: A, B
Molecule details ›
Chains: A, B
Length: 381 amino acids
Theoretical weight: 44.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin

Ligands and Environments

6 bound ligands:
Ligand NI 2 x NI
Ligand PYR 4 x PYR
Ligand DMS 2 x DMS
Ligand EDO 17 x EDO
Ligand ZN 2 x ZN
Ligand 1KA 1 x 1KA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 100.45Å b: 148.83Å c: 57.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.236
Expression system: Escherichia coli BL21(DE3)

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