› 4rn0

X-ray diffraction
1.76Å resolution

Crystal structure of S39D HDAC8 in complex with a largazole analogue.

Released:
DOI: 10.2210/pdb4rn0/pdb
PDB entry 4rn0 coloured by chain, front view.
PDB entry 4rn0 coloured by chain, side view.
PDB entry 4rn0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8.
Decroos C, Clausen DJ, Haines BE, Wiest O, Williams RM, Christianson DW
Biochemistry 54 2126-35 (2015)
PMID: 25793284

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:
monomeric (preferred)
homo dimer
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: 43.26 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

Ligands and Environments

5 bound ligands:
Ligand L6G 2 x L6G
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand IMD 1 x IMD
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 53.921Å b: 85.006Å c: 94.665Å
α: 90° β: 100.33° γ: 90°
R-values:
R R work R free
0.138 0.137 0.162
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
8 more

6 mentions without citation

Azumamides A-E: Isolation, Synthesis, Biological Activity, and Structure-Activity Relationship.
Jo et al. (2022)
5 more