› 4qa7

X-ray diffraction
2.31Å resolution

Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate

Released:
DOI: 10.2210/pdb4qa7/pdb
PDB entry 4qa7 coloured by chain, front view.
PDB entry 4qa7 coloured by chain, side view.
PDB entry 4qa7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Compromised structure and function of HDAC8 mutants identified in Cornelia de Lange Syndrome spectrum disorders.
Decroos C, Bowman CM, Moser JA, Christianson KE, Deardorff MA, Christianson DW
ACS Chem Biol 9 2157-64 (2014)
PMID: 25075551

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165087 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 8 Chain: A
Molecule details ›
Chain: A
Length: 389 amino acids
Theoretical weight: 43.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BY41 (Residues: 1-377; Coverage: 100%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain
tetrapeptide substrate Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 680 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand MCM 1 x MCM
Ligand GOL 1 x GOL
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P3121
Unit cell:
a: 80.406Å b: 80.406Å c: 106.063Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.204 0.242
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

HDAC8: a multifaceted target for therapeutic interventions.
Chakrabarti et al. (2015)
12 more

2 mentions without citation

Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders.
Osko et al. (2021)
1 more