› 5thu

X-ray diffraction
1.95Å resolution

Crystal Structure of G304A HDAC8 in complex with M344

Released:
DOI: 10.2210/pdb5thu/pdb
PDB entry 5thu coloured by chain, front view.
PDB entry 5thu coloured by chain, side view.
PDB entry 5thu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8.
Porter NJ, Christianson NH, Decroos C, Christianson DW
Biochemistry 55 6718-6729 (2016)
PMID: 27933794

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 389 amino acids
Theoretical weight: 43.25 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

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand B3N 2 x B3N
Ligand GGG 1 x GGG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL14-1
Spacegroup: P21
Unit cell:
a: 53.5Å b: 83.95Å c: 98.4Å
α: 90° β: 101.83° γ: 90°
R-values:
R R work R free
0.177 0.175 0.2
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

3 mentions without citation

Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8.
Porter et al. (2016)
2 more