Crystal structure of human SIRT3 in complex with native alkylimidate formed from acetyl-lysine ACS2-peptide crystallized in presence of the inhibitor ex-527

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).

Ligands and binding sites

• XYQ · (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl acetate · ligand · chains A, B
• ZN · Zinc ion · metal · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A
• EDO · 1,2-ethanediol · additive · 7 copies · chains A
• GOL · Glycerol · additive · 3 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 538 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 4BVG · Crystal structure of human SIRT3 in complex with native alkylimidate formed from… · 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 0.98
• Q9NUB1 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a synthetase 2-like, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.46

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
• Every structure of UniProt Q9NUB1
• Elsewhere: RCSB PDB 4BVG · PDBe 4BVG · UniProt Q9NTG7 · UniProt Q9NUB1