› 2gh6

X-ray diffraction
2.2Å resolution

Crystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-oxo-N-phenylnonan amide bound

Released:
DOI: 10.2210/pdb2gh6/pdb
PDB entry 2gh6 coloured by chain, front view.
PDB entry 2gh6 coloured by chain, side view.
PDB entry 2gh6 coloured by chain, top view.
Source organism: Alcaligenaceae bacterium FB188
Primary publication:
Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor.
Nielsen TK, Hildmann C, Riester D, Wegener D, Schwienhorst A, Ficner R
Acta Crystallogr Sect F Struct Biol Cryst Commun 63 270-3 (2007)
PMID: 17401192

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-180684 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase-like amidohydrolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 369 amino acids
Theoretical weight: 39.42 KDa
Source organism: Alcaligenaceae bacterium FB188
Expression system: Escherichia coli
UniProt:
  • Canonical: Q70I53 (Residues: 2-369; Coverage: 100%)
Gene names: hdaH, hdaH1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand CF3 4 x CF3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 68.507Å b: 94.897Å c: 123.301Å
α: 90° β: 104.28° γ: 90°
R-values:
R R work R free
0.161 0.158 0.214
Expression system: Escherichia coli

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Citations

1 review citation

Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design.
Hodawadekar et al. (2007)
8 other articles

4 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
3 more