› 4qa6

X-ray diffraction
2.05Å resolution

Crystal structure of I243N/Y306F HDAC8 in complex with a tetrapeptide substrate

Released:
DOI: 10.2210/pdb4qa6/pdb
PDB entry 4qa6 coloured by chain, front view.
PDB entry 4qa6 coloured by chain, side view.
PDB entry 4qa6 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-165086 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 389 amino acids
Theoretical weight: 43.22 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 Chains: C, D
Molecule details ›
Chains: C, D
Length: 5 amino acids
Theoretical weight: 680 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 51.832Å b: 85.071Å c: 94.444Å
α: 90° β: 97.55° γ: 90°
R-values:
R R work R free
0.182 0.181 0.212
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

1 mention without citation

Preparation of a new construct of human histone deacetylase 8 for the crystallization of enzyme-inhibitor complexes.
Porter et al. (2019)