› 7w3l

X-ray diffraction
2.51Å resolution

Crystal structure of LSD1 in complex with cis-4-Br-2,5-F2-PCPA (S1024)

Released:
DOI: 10.2210/pdb7w3l/pdb
PDB entry 7w3l coloured by chain, front view.
PDB entry 7w3l coloured by chain, side view.
PDB entry 7w3l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Niwa H, Watanabe C, Sato S, Harada T, Watanabe H, Tabusa R, Fukasawa S, Shiobara A, Hashimoto T, Ohno O, Nakamura K, Tsuganezawa K, Tanaka A, Shirouzu M, Honma T, Matsuno K, Umehara T
ACS Med Chem Lett 13 1485-1492 (2022)

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

4 bound ligands:
Ligand FAD 1 x FAD
Ligand 8A2 1 x 8A2
Ligand TLA 1 x TLA
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P6122
Unit cell:
a: 186.433Å b: 186.433Å c: 107.457Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.178 0.216
Expression system: Escherichia coli

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