› 4gd4

X-ray diffraction
2.33Å resolution

Crystal Structure of JMJD2A Complexed with Inhibitor

Released:
DOI: 10.2210/pdb4gd4/pdb
PDB entry 4gd4 coloured by chain, front view.
PDB entry 4gd4 coloured by chain, side view.
PDB entry 4gd4 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: King ONF, Krojer T, Arrowsmith CH, Edwards A, Bountra C, McDonough MA, Schofield CJ, Structural Genomics Consortium (SGC)

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
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin

Ligands and Environments

4 bound ligands:
Ligand NI 2 x NI
Ligand ZN 2 x ZN
Ligand CL 4 x CL
Ligand 0WS 2 x 0WS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21212
Unit cell:
a: 100.75Å b: 150.03Å c: 57.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.218
Expression system: Escherichia coli

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