› 2xaj

X-ray diffraction
3.3Å resolution

Crystal structure of LSD1-CoREST in complex with (-)-trans-2- phenylcyclopropyl-1-amine

Released:
DOI: 10.2210/pdb2xaj/pdb
PDB entry 2xaj coloured by chain, front view.
PDB entry 2xaj coloured by chain, side view.
PDB entry 2xaj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Biochemical, structural, and biological evaluation of tranylcypromine derivatives as inhibitors of histone demethylases LSD1 and LSD2.
Binda C, Valente S, Romanenghi M, Pilotto S, Cirilli R, Karytinos A, Ciossani G, Botrugno OA, Forneris F, Tardugno M, Edmondson DE, Minucci S, Mattevi A, Mai A
J Am Chem Soc 132 6827-33 (2010)
PMID: 20415477

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 analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129967 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 852 amino acids
Theoretical weight: 93.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 1-852; Coverage: 100%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
Structure domains:
REST corepressor 1 Chain: B
Molecule details ›
Chain: B
Length: 482 amino acids
Theoretical weight: 53.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKL0 (Residues: 4-485; Coverage: 99%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains:
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1

Ligands and Environments

2 bound ligands:
Ligand FAD 1 x FAD
Ligand TCA 1 x TCA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: I222
Unit cell:
a: 119.075Å b: 179.782Å c: 235.481Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.227
Expression system: Escherichia coli

Quick links

Citations

62 review citations

Epigenetic protein families: a new frontier for drug discovery.
Arrowsmith et al. (2012)
61 more

9 mentions without citation

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