Acid proteinase (penicillopepsin) (E.C.3.4.23.20) complex with phosphonate inhibitor: METHYL[CYCLO-7[(2R)-((N-valyl) amino)-2- (hydroxyl-(1S)-1-methyoxycarbonyl-2-phenylethoxy) phosphinyloxy- ethyl]-1-naphthaleneacetamide], sodium salt

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 47% strand (DSSP).

Ligands and binding sites

• PP6 · Methyl[cyclo-7[(2R)-((N-valyl)amino)-2-(hydroxyl-(1S)-1-methyloxycarbonyl-2-phenylethoxy)phosphinyloxy-ethyl]-1-naphthaleneacetamide] · ligand · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
• SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 2 glycan, 1 disulfide (O-glycosylation, disulfide).

Compared structures

• 2WEA · Acid proteinase (penicillopepsin) (E.C.3.4.23.20) complex with phosphonate inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
• P00798 · AlphaFold monomer V2.0 prediction for penicillopepsin-1 (P00798) · a predicted model of the same protein · chain A 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 P00798
• Elsewhere: RCSB PDB 2WEA · PDBe 2WEA · UniProt P00798