Crystal structure of cathepsin a, complexed with compound 1

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).

Ligands and binding sites

• 6KZ · N-[(2S)-4-methyl-1-oxidanylidene-1-[[(1R,2S)-1-oxidanyl-1-(5-phenyl-1,2,4-oxadiazol-3-yl)butan-2-yl]amino]pentan-2-yl]morpholine-4-carboxamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• CD · Cadmium ion · metal · 7 copies · 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: 4 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 4CIA · Crystal structure of cathepsin A, complexed with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00
• P10619 · AlphaFold monomer V2.0 prediction for lysosomal protective protein (P10619) · 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 P10619
• Elsewhere: RCSB PDB 4CIA · PDBe 4CIA · UniProt P10619