Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide tert-butyl-gly-L-pro-L-ile (tbu-gpi)

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).

Ligands and binding sites

• 0QG · 3-methyl-L-valyl-L-prolyl-L-isoleucine · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 2 copies
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 2289 Ų buried · 39 hydrogen bonds · protein-protein
• C–D · 2281 Ų buried · 41 hydrogen bonds · protein-protein
• B–D · 597 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 587 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 glycan, 16 disulfide, 4 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

• 2AJB · Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide… · the same entry in another collection · chain D against D, TM-score 1.00
• P22411 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P22411) · a predicted model of the same protein · chain B 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 P22411
• Elsewhere: RCSB PDB 2AJB · PDBe 2AJB · UniProt P22411