› 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:
DOI: 10.2210/pdb5icn/pdb
PDB entry 5icn coloured by chain, front view.
PDB entry 5icn coloured by chain, side view.
PDB entry 5icn coloured by chain, top view.
Source organisms:
Primary publication:
Insights into the activation mechanism of class I HDAC complexes by inositol phosphates.
Watson PJ, Millard CJ, Riley AM, Robertson NS, Wright LC, Godage HY, Cowley SM, Jamieson AG, Potter BV, Schwabe JW
Nat Commun 7 11262 (2016)
PMID: 27109927

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-165783 (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:
Structure domains: Homeodomain-like
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:
Ligand IHP 1 x IHP
Ligand ZN 1 x ZN
Ligand K 2 x K
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

Quick links

Citations

26 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
25 more

46 mentions without citation

The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex.
Leighton et al. (2020)
45 more