› 3kv9

X-ray diffraction
2.29Å resolution

Structure of KIAA1718 Jumonji domain

Released:
DOI: 10.2210/pdb3kv9/pdb
PDB entry 3kv9 coloured by chain, front view.
PDB entry 3kv9 coloured by chain, side view.
PDB entry 3kv9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X
Nat Struct Mol Biol 17 38-43 (2010)
PMID: 20023638

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-180579 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 7A Chain: A
Molecule details ›
Chain: A
Length: 397 amino acids
Theoretical weight: 46.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ZMT4 (Residues: 92-488; Coverage: 42%)
Gene names: JHDM1D, KDM7, KDM7A, KIAA1718
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6122
Unit cell:
a: 77.9Å b: 77.9Å c: 289.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.222 0.258
Expression system: Escherichia coli

Quick links

Citations

83 review citations

Histone methylation: a dynamic mark in health, disease and inheritance.
Greer et al. (2012)
82 more

3 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
2 more