› 4rn1

X-ray diffraction
2.18Å resolution

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

Released:
DOI: 10.2210/pdb4rn1/pdb
PDB entry 4rn1 coloured by chain, front view.
PDB entry 4rn1 coloured by chain, side view.
PDB entry 4rn1 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

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: 43.26 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 ZN 2 x ZN
Ligand K 4 x K
Ligand L8G 2 x L8G
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: 54.051Å b: 85.124Å c: 95.354Å
α: 90° β: 100.21° γ: 90°
R-values:
R R work R free
0.184 0.182 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

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

3 mentions without citation

Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8.
Decroos et al. (2015)
2 more