Crystal structure of A188T/Y306F HDAC8 in complex with a tetrapeptide substrate

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 13% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains C, 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
• MG · Magnesium ion · metal · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 1048 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 450 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 447 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 171 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 103 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4QA5 · Crystal structure of A188T/Y306F HDAC8 in complex with a tetrapeptide substrate · 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 A 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 4QA5 · PDBe 4QA5 · UniProt Q9BY41