› 6dvm

X-ray diffraction
1.47Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122

Released:
DOI: 10.2210/pdb6dvm/pdb
PDB entry 6dvm coloured by chain, front view.
PDB entry 6dvm coloured by chain, side view.
PDB entry 6dvm coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.
Porter NJ, Osko JD, Diedrich D, Kurz T, Hooker JM, Hansen FK, Christianson DW
J Med Chem 61 8054-8060 (2018)
PMID: 30118224

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 364 amino acids
Theoretical weight: 40.29 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 440-798; Coverage: 33%)
Gene name: hdac6
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 HBJ 4 x HBJ
Ligand EDO 13 x EDO
Ligand BTB 1 x BTB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 78.45Å b: 95.18Å c: 98.03Å
α: 90° β: 98.87° γ: 90°
R-values:
R R work R free
0.149 0.148 0.17
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases.
Porter et al. (2019)
5 more

3 mentions without citation

Structural determinants of affinity and selectivity in the binding of inhibitors to histone deacetylase 6.
Osko et al. (2020)
2 more