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› 6hrq

X-ray diffraction
1.84Å resolution

Crystal structure of Schistosoma mansoni HDAC8 complexed with NCC-149

Released:
DOI: 10.2210/pdb6hrq/pdb
Model geometry
Fit model/data
PDB entry 6hrq coloured by chain, front view.
PDB entry 6hrq coloured by chain, side view.
PDB entry 6hrq 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: 
N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107599 (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 GM5 4 x GM5
Ligand DMF 28 x DMF
Ligand GOL 13 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P1
Unit cell:
a: 71.43Å b: 71.48Å c: 99.26Å
α: 78.11° β: 75.54° γ: 85.37°
R-values:
R R work R free
0.152 0.15 0.183
Expression system: Escherichia coli

Quick links

Citations

7 review citations

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

2 mentions without citation

Structure of the E. coli agmatinase, SPEB.
Chitrakar et al. (2021)
1 more