› 6pzs

X-ray diffraction
1.79Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JR005

Released:
DOI: 10.2210/pdb6pzs/pdb
PDB entry 6pzs coloured by chain, front view.
PDB entry 6pzs coloured by chain, side view.
PDB entry 6pzs coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6.
Osko JD, Porter NJ, Narayana Reddy PA, Xiao YC, Rokka J, Jung M, Hooker JM, Salvino JM, Christianson DW
J Med Chem 63 295-308 (2020)
PMID: 31793776

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
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 Chain: A
Molecule details ›
Chain: A
Length: 357 amino acids
Theoretical weight: 39.72 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 442-798; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand P7J 1 x P7J
Ligand CL 1 x CL
Ligand NO3 2 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Unit cell:
a: 51.65Å b: 83.67Å c: 94.779Å
α: 90° β: 90° γ: 90°
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Chasing a Breath of Fresh Air in Cystic Fibrosis (CF): Therapeutic Potential of Selective HDAC6 Inhibitors to Tackle Multiple Pathways in CF Pathophysiology.
Barone et al. (2022)
1 more

2 mentions without citation

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