› 6oda

X-ray diffraction
2.88Å resolution

Crystal structure of HDAC8 in complex with compound 2

Released:
DOI: 10.2210/pdb6oda/pdb
Model geometry
Data not analysed
Fit model/data
Data not analysed
PDB entry 6oda coloured by chain, front view.
PDB entry 6oda coloured by chain, side view.
PDB entry 6oda coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zheng X, Conti C, Caravella J, Zablocki M-M, Bair K, Barczak N, Han B, Lancia Jr D, Liu C, Martin M, Ng PY, Rudnitskaya A, Thomason JJ, Garcia-Dancey R, Hardy C, Lahdenranta J, Leng C, Li P, Pardo E, Saldahna A, Tan T, Toms AV, Yao L, Zhang C

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 8 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 413 amino acids
Theoretical weight: 45.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BY41 (Residues: 1-377; Coverage: 100%)
Gene names: CDA07, HDAC8, HDACL1
Sequence domains: Histone deacetylase domain

Ligands and Environments

3 bound ligands:
Ligand C7 3 x C7
Ligand ZN 3 x ZN
Ligand K 6 x K
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 87.75Å b: 91.29Å c: 92.7Å
α: 90° β: 94.09° γ: 90°
R-values:
R R work R free
0.201 0.199 0.249
Expression system: Escherichia coli BL21(DE3)

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