› 5wgm

X-ray diffraction
1.75Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ACY-1083

Released:
DOI: 10.2210/pdb5wgm/pdb
PDB entry 5wgm coloured by chain, front view.
PDB entry 5wgm coloured by chain, side view.
PDB entry 5wgm coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.
Porter NJ, Mahendran A, Breslow R, Christianson DW
Proc Natl Acad Sci U S A 114 13459-13464 (2017)
PMID: 29203661

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
Molecule details ›
Chains: A, B, C
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 3 x ZN
Ligand K 6 x K
Ligand AH7 3 x AH7
Ligand EDO 37 x EDO
Ligand PGE 2 x PGE
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2221
Unit cell:
a: 97.813Å b: 174.304Å c: 149.064Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.185
Expression system: Escherichia coli

Quick links

Citations

9 review citations

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

6 mentions without citation

A patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2014-2019).
Shen et al. (2020)
5 more