› 2z3y

X-ray diffraction
2.25Å resolution

Crystal structure of Lysine-specific demethylase1

Released:
DOI: 10.2210/pdb2z3y/pdb
PDB entry 2z3y coloured by chain, front view.
PDB entry 2z3y coloured by chain, side view.
PDB entry 2z3y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.
Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S
Biochem Biophys Res Commun 366 15-22 (2008)
PMID: 18039463

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: 662 amino acids
Theoretical weight: 73.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O60341 (Residues: 172-833; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand F2N 1 x F2N
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P6122
Unit cell:
a: 185.742Å b: 185.742Å c: 108.725Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.218 0.255
Expression system: Escherichia coli BL21

Quick links

Citations

23 review citations

Central role of Snail1 in the regulation of EMT and resistance in cancer: a target for therapeutic intervention.
Kaufhold et al. (2014)
22 more

9 mentions without citation

Targeting histone lysine demethylases - progress, challenges, and the future.
Thinnes et al. (2014)
8 more