Acid proteinase (penicillopepsin) (E.C.3.4.23.20) complex with phosphonate inhibitor: METHYL(2S)-[1-(((N-formyl)-L-VALYL)AMINO-2-(2- NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-phenylpropanoate, sodium salt

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 48% strand (DSSP).

Ligands and binding sites

• PP4 · Methyl (2S)-[1-((N-formyl)-L-valyl)amino-2-(2-naphthyl)ethyl)hydroxyphosphinyloxy]-3-phenyl propanoate · 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

• 2WEB · 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 0.99

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 2WEB · PDBe 2WEB · UniProt P00798