› 2h94

X-ray diffraction
2.9Å resolution

Crystal Structure and Mechanism of human Lysine-Specific Demethylase-1

Released:
DOI: 10.2210/pdb2h94/pdb
PDB entry 2h94 coloured by chain, front view.
PDB entry 2h94 coloured by chain, side view.
PDB entry 2h94 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and mechanism of human lysine-specific demethylase-1.
Stavropoulos P, Blobel G, Hoelz A
Nat Struct Mol Biol 13 626-32 (2006)
PMID: 16799558

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + acceptor + H(2)O = a [histone H3]-N(6)-methyl-L-lysine(4) + formaldehyde + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129945 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 664 amino acids
Theoretical weight: 73.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 172-835; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand HG 3 x HG
Ligand FAD 1 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P6122
Unit cell:
a: 187.943Å b: 187.943Å c: 108.741Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.281 0.229 0.281
Expression system: Escherichia coli

Quick links

Citations

60 review citations

Molecular mechanisms and potential functions of histone demethylases.
Kooistra et al. (2012)
59 more

11 mentions without citation

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Black et al. (2012)
10 more