Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose

Structure

x-ray diffraction · resolution 1.9 · 2 distinct chains · 41% helix, 20% strand (DSSP).

Ligands and binding sites

• APR · Adenosine-5-diphosphoribose · ligand · chains A, D
• 3OD · (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4,5-dihydroxytetrahydrofuran-3-yl acetate · ligand · chains B, E
• ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 584 Ų buried · 7 hydrogen bonds · protein-protein
• B–E · 505 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 480 Ų buried · 8 hydrogen bonds · protein-protein
• A–E · 115 Ų buried · 0 hydrogen bonds · protein-protein
• B–D · 65 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 2H59 · SIR2 H116A-deacetylated P53 peptide-3'-O-acetyl ADP ribose · the same entry in another collection · chain A against A, TM-score 1.00
• Q9WYW0 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase (Q9WYW0) · 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 Q9WYW0
• Every structure of UniProt Q9NP68
• Elsewhere: RCSB PDB 2H59 · PDBe 2H59 · UniProt Q9WYW0 · UniProt Q9NP68