Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with rts-V5

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).

Ligands and binding sites

• FGY · N-(2,2-dimethylpropyl)-N~2~-[4-(hydroxycarbamoyl) benzene-1-carbonyl]-L-asparaginyl-N-benzyl-L-alaninamide · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 9 copies · chains A, B

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.

• A–B · 112 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6CW8 · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with… · the same entry in another collection · 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 A7YT55
• Elsewhere: RCSB PDB 6CW8 · PDBe 6CW8 · UniProt A7YT55