› 6kgr

X-ray diffraction
2.32Å resolution

LSD1-FCPA-MPE N5 adduct model

Released:
DOI: 10.2210/pdb6kgr/pdb
PDB entry 6kgr coloured by chain, front view.
PDB entry 6kgr coloured by chain, side view.
PDB entry 6kgr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Niwa H, Sato S, Handa N, Sengoku T, Umehara T, Yokoyama S
ChemMedChem 15 787-793 (2020)
PMID: 32166890

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:
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: 669 amino acids
Theoretical weight: 74.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 172-833; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand MPD 1 x MPD
Ligand DJC 1 x DJC
Ligand FAD 1 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P6122
Unit cell:
a: 185.268Å b: 185.268Å c: 109.327Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.168 0.198
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

MicroRNA-137-mediated inhibition of lysine-specific demethylase-1 prevents against rheumatoid arthritis in an association with the REST/mTOR axis.
Sun et al. (2021)
4 more