› 6k3e

X-ray diffraction
2.87Å resolution

LSD1/Co-Rest structure with an inhibitor

Released:
DOI: 10.2210/pdb6k3e/pdb
PDB entry 6k3e coloured by chain, front view.
PDB entry 6k3e coloured by chain, side view.
PDB entry 6k3e coloured by chain, top view.
Source organism: Homo sapiens
Entry author: Wang J

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: 662 amino acids
Theoretical weight: 73.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60341 (Residues: 172-833; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
REST corepressor 1 Chain: B
Molecule details ›
Chain: B
Length: 140 amino acids
Theoretical weight: 15.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKL0 (Residues: 311-443; Coverage: 27%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains:

Ligands and Environments

9 bound ligands:
Ligand CW0 1 x CW0
Ligand DTT 1 x DTT
Ligand ACT 2 x ACT
Ligand MLA 3 x MLA
Ligand GOL 4 x GOL
Ligand D3U 1 x D3U
Ligand EDO 12 x EDO
Ligand PEG 3 x PEG
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: I222
Unit cell:
a: 121.51Å b: 179.44Å c: 234.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.223
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

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