Crystal structure of human SIRT3 in complex with the inhibitor ex-527 and 2'-O-acetyl-ADP-ribose

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).

Ligands and binding sites

• OCZ · (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide · ligand · 3 copies · chains A, B, C
• OAD · 2'-O-acetyl adenosine-5-diphosphoribose · ligand · 2 copies · chains A, C
• AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains B
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 5 copies · chains B, C
• GOL · Glycerol · additive · chains C

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–B · 735 Ų buried · 18 hydrogen bonds · protein-protein
• B–C · 644 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 4BVH · Crystal structure of human SIRT3 in complex with the inhibitor ex-527 and… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9NTG7
• Elsewhere: RCSB PDB 4BVH · PDBe 4BVH · UniProt Q9NTG7