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

Structure

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

Ligands and binding sites

• IVV · N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)-(2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]-3-methylbutyl}-L-valinamide · ligand · chains E
• HSY · alpha-L-xylopyranose · ligand · chains E
• MAN · alpha-D-mannopyranose · sugar · chains E
• SO4 · Sulfate ion · ion · chains E
• DMF · Dimethylformamide · additive · 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: 1 covalent, 1 disulfide, 1 glycan (covalent ligand, disulfide, O-glycosylation).

Compared structures

• 1PPK · 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 1PPK · PDBe 1PPK · UniProt P00798