Human SIRT2 in complex with ADP ribose and nicotinamide

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Ligands and binding sites

• 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 · 2 copies · chains A, B
• NCA · Nicotinamide · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains A
• PGE · Triethylene glycol · additive · chains B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 994 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 4RMJ · Human Sirt2 in complex with ADP ribose and nicotinamide · the same entry in another collection · chain A against A, TM-score 1.00
• Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q8IXJ6
• Elsewhere: RCSB PDB 4RMJ · PDBe 4RMJ · UniProt Q8IXJ6