S1 nuclease from aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 4% strand (DSSP).

Ligands and binding sites

• AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
• ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• ZN · Zinc ion · metal · 6 copies · chains A, B
• CA · Calcium ion · metal · 5 copies · chains A, B
• NA · Sodium ion · metal · 3 copies · chains A, B
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B

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 · 725 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 5FBB · S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine… · the same entry in another collection · chain A against A, TM-score 1.00
• 5FBB · S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine… · the same entry in another collection · chain A against A, TM-score 1.00
• P24021 · AlphaFold monomer V2.0 prediction for nuclease S1 (P24021) · 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 P24021
• Elsewhere: RCSB PDB 5FBB · PDBe 5FBB · UniProt P24021