› 5ivc

X-ray diffraction
1.57Å resolution

Linked KDM5A Jmj Domain Bound to the Inhibitor N3 (4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid)

Released:
DOI: 10.2210/pdb5ivc/pdb
PDB entry 5ivc coloured by chain, front view.
PDB entry 5ivc coloured by chain, side view.
PDB entry 5ivc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X
Cell Chem Biol 23 769-781 (2016)
PMID: 27427228

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + 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-151436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5A Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29375 (Residues: 1-588; Coverage: 19%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Sequence domains:
Structure domains: Cupin

Ligands and Environments

4 bound ligands:
Ligand 6E7 1 x 6E7
Ligand MN 1 x MN
Ligand EDO 3 x EDO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 116.216Å b: 62.295Å c: 46.519Å
α: 90° β: 92.18° γ: 90°
R-values:
R R work R free
0.167 0.166 0.184
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
14 more

1 mention without citation

Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Horton et al. (2016)