› 8eqi

X-ray diffraction
2Å resolution

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0

Released:
DOI: 10.2210/pdb8eqi/pdb
PDB entry 8eqi coloured by chain, front view.
PDB entry 8eqi coloured by chain, side view.
PDB entry 8eqi coloured by chain, top view.
Source organisms:
Primary publication:
Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6.
Watson PR, Gupta S, Hosseinzadeh P, Brown BP, Baker D, Christianson DW
ACS Chem Biol (2023)
PMID: 37027789

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-230676 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
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
Cyclopeptide des4.2.0 Chains: F, G
Molecule details ›
Chains: F, G
Length: 8 amino acids
Theoretical weight: 1.02 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
3 modified residues:
Ligand DGL 2 x DGL
Ligand DSN 2 x DSN
Ligand DAS 2 x DAS

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: P212121
Unit cell:
a: 57.45Å b: 92.03Å c: 153.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.236 0.272
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Crystal structure of histone deacetylase 6 complexed with (R)-lipoic acid, an essential cofactor in central carbon metabolism.
Watson et al. (2023)