X-ray structure of human glutamate carboxypeptidase II (gcpii) in complex with a urea based inhibitor psma 1007

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).

Ligands and binding sites

• 9OT · (2~{S})-2-[[(2~{S})-6-[[(2~{S})-2-[[4-[[[(2~{S})-2-[[(2~{S})-2-[(6-fluoranylpyridin-3-yl)carbonylamino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]methyl]phenyl]carbonylamino]-3-naphthalen-2-yl-propanoyl]amino]-1-oxidanyl-1-oxidanylidene-hexan-2-yl]carbamoylamino]pentanedioic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Modifications

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

Compared structures

• 5O5T · X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea… · 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 5O5T · PDBe 5O5T · UniProt Q04609