› 5ivb

X-ray diffraction
1.39Å resolution

A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate

Released:
DOI: 10.2210/pdb5ivb/pdb
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PDB entry 5ivb coloured by chain, front view.
PDB entry 5ivb coloured by chain, side view.
PDB entry 5ivb 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

3 bound ligands:
Ligand AKG 1 x AKG
Ligand MN 1 x MN
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 116.34Å b: 62.199Å c: 46.751Å
α: 90° β: 92.63° γ: 90°
R-values:
R R work R free
0.183 0.182 0.214
Expression system: Escherichia coli BL21(DE3)

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Citations

15 review citations

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

3 mentions without citation

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

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