PDBe 5icn

X-ray diffraction
3.3Å resolution

HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4

Released:

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Metastasis-associated protein MTA1 Chain: A
Molecule details ›
Chain: A
Length: 195 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13330 (Residues: 162-354; Coverage: 27%)
Gene name: MTA1
Sequence domains:
Histone deacetylase 1 Chain: B
Molecule details ›
Chain: B
Length: 376 amino acids
Theoretical weight: 43.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13547 (Residues: 1-376; Coverage: 78%)
Gene names: HDAC1, RPD3L1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain
GLY-ALA-6A0-ARG-HIS Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 984 Da
Source organism: synthetic construct
Expression system: synthetic construct

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P3221
Unit cell:
a: 107.815Å b: 107.815Å c: 134.161Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.257 0.255 0.299
Expression systems:
  • Homo sapiens
  • synthetic construct