› 6wyp

X-ray diffraction
2.4Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with SAHA-BPyne

Released:
DOI: 10.2210/pdb6wyp/pdb
PDB entry 6wyp coloured by chain, front view.
PDB entry 6wyp coloured by chain, side view.
PDB entry 6wyp coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
Osko JD, Christianson DW
Acta Crystallogr F Struct Biol Commun 76 428-437 (2020)
PMID: 32880591

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 Chain: A
Molecule details ›
Chain: A
Length: 380 amino acids
Theoretical weight: 42.04 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 61-419; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand UFS 1 x UFS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: C2221
Unit cell:
a: 66.029Å b: 95.17Å c: 119.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.243
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6.
Osko et al. (2020)