X-ray structure of a cyclic statine inhibitor pd-129,541 bound to yeast proteinase a

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 45% strand (DSSP).

Ligands and binding sites

• 0GM · N-[(5S,9S,10S,13S)-9-hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16-tetraoxo-3,6,11,17-tetraazabicyclo[17.3.1]tricosa-1(23),19,21-trien-13-yl]-3-(naphthalen-1-yl)-2-(naphthalen-1-ylmethyl)propanamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar

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 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 1FQ5 · X-ray structure of a cyclic statine inhibitor PD-129,541 bound to yeast proteinase A · the same entry in another collection · chain A against A, TM-score 1.00
• P07267 · AlphaFold monomer V2.0 prediction for saccharopepsin (P07267) · 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 P07267
• Elsewhere: RCSB PDB 1FQ5 · PDBe 1FQ5 · UniProt P07267