› 5it3

X-ray diffraction
1.4Å resolution

Swirm domain of human Lsd1

Released:
DOI: 10.2210/pdb5it3/pdb
PDB entry 5it3 coloured by chain, front view.
PDB entry 5it3 coloured by chain, side view.
PDB entry 5it3 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Jeffrey PD, Yuan P

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129968 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific histone demethylase 1A Chains: A, B
Molecule details ›
Chains: A, B
Length: 85 amino acids
Theoretical weight: 9.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O60341 (Residues: 183-267; Coverage: 10%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains: SWIRM domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F2
Spacegroup: P21212
Unit cell:
a: 57.17Å b: 49.97Å c: 48.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.194
Expression system: Escherichia coli K-12

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