Crystal structure of glutamate carboxypeptidase II in a complex with urea-based inhibitor

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Ligands and binding sites

• J31 · N-{[(1S)-1-carboxy-5-{[2-({4,44-dioxo-48-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-7,10,13,16,19,22,25,28,31,34,37,40-dodecaoxa-3,43-diazaoctatetracont-1-yl}oxy)benzoyl]amino}pentyl]carbamoyl}-L-glutamic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• ZN · Zinc ion · metal · 2 copies · chains A
• CA · Calcium ion · metal · chains A
• CL · Chloride ion · ion · chains A

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

Pockets

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

Modifications

Observed in the structure: 7 glycan (N-glycosylation).

Compared structures

• 4NGP · Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• Q04609 · AlphaFold monomer V2.0 prediction for glutamate carboxypeptidase 2 (Q04609) · a predicted model of the same protein · chain A 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 Q04609
• Elsewhere: RCSB PDB 4NGP · PDBe 4NGP · UniProt Q04609