Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with trifluoroketone transition state analogue

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).

Ligands and binding sites

• FKS · 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol · ligand · 2 copies · chains D, A
• K · Potassium ion · metal · 4 copies · chains D, A
• ZN · Zinc ion · metal · 2 copies · chains D, A
• BR · Bromide ion · ion · 7 copies · chains D, A
• EDO · 1,2-ethanediol · additive · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• D–A · 124 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5EFH · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · chain D against D, 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 A7YT55
• Elsewhere: RCSB PDB 5EFH · PDBe 5EFH · UniProt A7YT55