› 5dc6

X-ray diffraction
1.55Å resolution

Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapeptide substrate

Released:
DOI: 10.2210/pdb5dc6/pdb
PDB entry 5dc6 coloured by chain, front view.
PDB entry 5dc6 coloured by chain, side view.
PDB entry 5dc6 coloured by chain, top view.
Source organisms:
Primary publication:
General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Gantt SM, Decroos C, Lee MS, Gullett LE, Bowman CM, Christianson DW, Fierke CA
Biochemistry 55 820-32 (2016)
PMID: 26806311

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-165550 (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
Fluor-de-Lys tetrapeptide assay substrate Chains: C, D
Molecule details ›
Chains: C, D
Length: 6 amino acids
Theoretical weight: 837 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand K 2 x K
Ligand GOL 3 x GOL
1 modified residue:
Ligand ALY 4 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 82.332Å b: 98.206Å c: 104.281Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.147 0.166
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases.
Porter et al. (2019)
8 more

3 mentions without citation

General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Gantt et al. (2016)
2 more