› 6csp

X-ray diffraction
1.24Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with cyclohexenylhydroxamate

Released:
DOI: 10.2210/pdb6csp/pdb
PDB entry 6csp coloured by chain, front view.
PDB entry 6csp coloured by chain, side view.
PDB entry 6csp coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6.
Porter NJ, Wagner FF, Christianson DW
Biochemistry 57 3916-3924 (2018)
PMID: 29775292

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-514703 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
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

6 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
Ligand CL 4 x CL
Ligand FBM 2 x FBM
Ligand EDO 22 x EDO
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 74.7Å b: 91.83Å c: 96.549Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.128 0.127 0.153
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases.
Porter et al. (2019)
17 other articles

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