› 6htg

X-ray diffraction
1.94Å resolution

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 4

Released:
DOI: 10.2210/pdb6htg/pdb
PDB entry 6htg coloured by chain, front view.
PDB entry 6htg coloured by chain, side view.
PDB entry 6htg coloured by chain, top view.
Source organism: Schistosoma mansoni
Primary publication:
Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Marek M, Shaik TB, Heimburg T, Chakrabarti A, Lancelot J, Ramos-Morales E, Da Veiga C, Kalinin D, Melesina J, Robaa D, Schmidtkunz K, Suzuki T, Holl R, Ennifar E, Pierce RJ, Jung M, Sippl W, Romier C
J Med Chem 61 10000-10016 (2018)
PMID: 30347148

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-107598 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
histone deacetylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 447 amino acids
Theoretical weight: 50.58 KDa
Source organism: Schistosoma mansoni
Expression system: Escherichia coli
UniProt:
  • Canonical: A5H660 (Residues: 1-440; Coverage: 100%)
Gene name: HDAC8
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

5 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand T61 4 x T61
Ligand DMF 25 x DMF
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 70.66Å b: 70.64Å c: 98.33Å
α: 77.73° β: 75.86° γ: 85.63°
R-values:
R R work R free
0.171 0.169 0.215
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Next-generation of selective histone deacetylase inhibitors.
Yang et al. (2019)
6 more