Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide

Structure

x-ray diffraction · resolution 1.7 · 3 distinct chains · 32% helix, 21% strand (DSSP).

Ligands and binding sites

• WSN · N-[(2R)-4-amino-1-imino-4-oxobutan-2-yl]-1-(1-{4-[(2,4-difluorophenyl)methoxy]phenyl}cyclopropane-1-carbonyl)-L-prolinamide · ligand · 3 copies · chains A, C, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A, C
• MG · Magnesium ion · metal · chains B
• SO4 · Sulfate ion · ion · chains C
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
• PG4 · Tetraethylene glycol · additive · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
• FLC · Citrate anion · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 533 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 330 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 300 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 3 glycan, 3 modified (covalent ligand, N-glycosylation, nonstandard).

Compared structures

• Q99538 · AlphaFold monomer V2.0 prediction for legumain (Q99538) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 Q99538
• Elsewhere: RCSB PDB 7FQJ · PDBe 7FQJ · UniProt Q99538