Crystal structure of piratoxin I (prtx-I) complexed to caffeic acid

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 7% strand (DSSP).

Ligands and binding sites

• DHC · Caffeic acid · ligand · 4 copies · chains B, A
• SO4 · Sulfate ion · ion · chains A
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 3 copies · chains B, A

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.

• B–A · 442 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

• 4YU7 · Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid · the same entry in another collection · chain B against B, TM-score 1.00
• P58399 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog piratoxin-1 (P58399) · a predicted model of the same protein · chain B 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 P58399
• Elsewhere: RCSB PDB 4YU7 · PDBe 4YU7 · UniProt P58399