Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues

Structure

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

Ligands and binding sites

• 0P1 · N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide · ligand · chains E
• MAN · alpha-D-mannopyranose · sugar · chains E
• ARA · alpha-L-arabinopyranose · sugar · chains E
• SO4 · Sulfate ion · ion · chains E

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

• 1PPM · Crystallographic analysis of transition-state mimics bound to penicillopepsin… · the same entry in another collection · chain E against E, TM-score 1.00
• P00798 · AlphaFold monomer V2.0 prediction for penicillopepsin-1 (P00798) · a predicted model of the same protein · chain E 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 1PPM · PDBe 1PPM · UniProt P00798