› 5h6r

X-ray diffraction
2.6Å resolution

Crystal structure of LSD1-CoREST in complex with peptide 13

Released:
DOI: 10.2210/pdb5h6r/pdb
PDB entry 5h6r coloured by chain, front view.
PDB entry 5h6r coloured by chain, side view.
PDB entry 5h6r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1.
Amano Y, Kikuchi M, Sato S, Yokoyama S, Umehara T, Umezawa N, Higuchi T
Bioorg Med Chem 25 2617-2624 (2017)
PMID: 28336409

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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-129949 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
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:
Structure 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:
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 21 amino acids
Theoretical weight: 2.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-21; Coverage: 15%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

2 bound ligands:
Ligand FAD 1 x FAD
Ligand GOL 2 x GOL
1 modified residue:
Ligand HSE 1 x HSE

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: I222
Unit cell:
a: 121.674Å b: 178.374Å c: 234.848Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.231
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Peptides as epigenetic modulators: therapeutic implications.
Janssens et al. (2019)
5 other articles