› 3ewf

X-ray diffraction
2.5Å resolution

Crystal Structure Analysis of human HDAC8 H143A variant complexed with substrate.

Released:
DOI: 10.2210/pdb3ewf/pdb
PDB entry 3ewf coloured by chain, front view.
PDB entry 3ewf coloured by chain, side view.
PDB entry 3ewf coloured by chain, top view.
Source organisms:
Primary publication:
Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW
Biochemistry 47 13554-63 (2008)
PMID: 19053282

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

Assemblies composition:
hetero octamer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163519 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 8 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 388 amino acids
Theoretical weight: 43.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BY41 (Residues: 1-377; Coverage: 100%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain
PEPTIDIC SUBSTRATE Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 5 amino acids
Theoretical weight: 680 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand K 8 x K
Ligand MCM 4 x MCM
1 modified residue:
Ligand ALY 8 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C, APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 82.903Å b: 91.844Å c: 196.577Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.198 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

HDACs and HDAC Inhibitors in Cancer Development and Therapy.
Li et al. (2016)
17 more

19 mentions without citation

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
18 more