Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate

Structure

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

Ligands and binding sites

• MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains B, A
• K · Potassium ion · metal · 2 copies · chains B
• ZN · Zinc ion · metal · chains B, A
• NO3 · Nitrate ion · ion · chains B
• GOL · Glycerol · additive · chains B
• PEG · Di(hydroxyethyl)ether · additive · chains B
• EDO · 1,2-ethanediol · additive · chains B

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

Interfaces

1 interface between chains.

• B–A · 289 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, acetylation).

Compared structures

• 5EFK · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant)… · the same entry in another collection · chain B against B, 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 5EFK · PDBe 5EFK · UniProt A7YT55