Crystal structure of human histone deacetylase 8 (HDAC8) E66D/Y306F double mutation complexed with a tetrapeptide substrate

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains C, B, D
• MCM · 7-amino-4-methyl-chromen-2-one · ligand · 2 copies · chains A, B, C, D
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
• EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
• GOL · Glycerol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 992 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 463 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 453 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 172 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 164 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).

Compared structures

• 7JVV · Crystal structure of human histone deacetylase 8 (HDAC8) E66D/Y306F double mutation… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9BY41
• Elsewhere: RCSB PDB 7JVV · PDBe 7JVV · UniProt Q9BY41