› 5vi6

X-ray diffraction
1.24Å resolution

Crystal structure of histone deacetylase 8 in complex with trapoxin A

Released:
DOI: 10.2210/pdb5vi6/pdb
PDB entry 5vi6 coloured by chain, front view.
PDB entry 5vi6 coloured by chain, side view.
PDB entry 5vi6 coloured by chain, top view.
Source organisms:
Primary publication:
Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8.
Porter NJ, Christianson DW
ACS Chem Biol 12 2281-2286 (2017)
PMID: 28846375

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166211 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 8 Chain: A
Molecule details ›
Chain: A
Length: 372 amino acids
Theoretical weight: 41.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BY41 (Residues: 8-377; Coverage: 98%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain
Trapoxin A Chain: B
Molecule details ›
Chain: B
Length: 4 amino acids
Theoretical weight: 639 Da
Source organism: Helicoma ambiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand K 2 x K
Ligand EDO 10 x EDO
Ligand DIO 2 x DIO
1 modified residue:
Ligand CPI 1 x CPI

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P32
Unit cell:
a: 50.98Å b: 50.98Å c: 116.517Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.122 0.121 0.143
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability.
Milazzo et al. (2020)
13 more

8 mentions without citation

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
7 more