Structural insights into substrate binding of brown spider venom class II phospholipases D

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Ligands and binding sites

• PLM · Palmitic acid · ligand · 3 copies · chains A
• DKA · Decanoic acid · ligand · 2 copies · chains A
• IPD · D-myo-inositol-1-phosphate · ligand · chains A
• OCA · Octanoic acid (caprylic acid) · ligand · chains A
• SHV · Heptanoic acid · ligand · chains A
• TDA · N-tridecanoic acid · ligand · chains A
• MG · Magnesium ion · metal · chains A
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
• GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 4RW3 · Structural insights into substrate binding of brown spider venom class II phospholipases D · the same entry in another collection · chain A against A, TM-score 1.00
• P0CE82 · AlphaFold monomer V2.0 prediction for dermonecrotic toxin lisictox- ALPHAIA1BII (P0CE82) · a predicted model of the same protein · chain A 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 P0CE82
• Elsewhere: RCSB PDB 4RW3 · PDBe 4RW3 · UniProt P0CE82