X-ray structure of glycol inhibitor pd-133,450 bound to saccharopepsin

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 44% strand (DSSP).

Ligands and binding sites

• GUP · alpha-L-gulopyranose · ligand · chains A
• 0QF · N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morp holin-4-ylsulfonyl)-L-phenylalaninamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets 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

• 1FQ6 · X-ray structure of glycol inhibitor pd-133,450 bound to saccharopepsin · 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 1FQ6 · PDBe 1FQ6 · UniProt P07267