SIRT2 in complex with a myristoyl peptide

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).

Ligands and binding sites

• 3Y0 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A, C
• ZN · Zinc ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · 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–C · 394 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4X3O · Sirt2 in complex with a myristoyl peptide · 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 0.98

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 4X3O · PDBe 4X3O · UniProt Q8IXJ6