S1 nuclease from aspergillus oryzae with unoccupied active site

Structure

x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
• ZN · Zinc ion · metal · 6 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 486 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5FB9 · S1 nuclease from Aspergillus oryzae with unoccupied active site · 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 B against A, TM-score 1.00

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 5FB9 · PDBe 5FB9 · UniProt P24021