Crystal structure of phospholipase A2 with inhibitor

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).

Ligands and binding sites

• 7W3 · 2-[2-methyl-3-oxamoyl-1-[[2-(trifluoromethyl) phenyl]methyl]indol-4-yl]oxyethanoic acid · ligand · chains A
• CA · Calcium ion · metal · chains A
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 5 copies · chains A
• GOL · Glycerol · additive · chains A
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 0 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

• 5Y5E · Crystal structure of phospholipase A2 with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NZK7 · AlphaFold monomer V2.0 prediction for group iie secretory phospholipase A2 (Q9NZK7) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9NZK7
• Elsewhere: RCSB PDB 5Y5E · PDBe 5Y5E · UniProt Q9NZK7