Porcine dipeptidyl peptidase IV (CD26) in complex with 7-benzyl-1,3- dimethyl-8-piperazin-1-yl-3,7-dihydro-purine-2,6-dione (bdpx)

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).

Ligands and binding sites

• SC3 · 7-benzyl-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-purine-2,6-dione · ligand · 8 copies · chains A, C, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
• 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, 15 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 2300 Ų buried · 41 hydrogen bonds · protein-protein
• C–D · 2294 Ų buried · 39 hydrogen bonds · protein-protein
• B–D · 597 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 595 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2AJ8 · Porcine dipeptidyl peptidase IV (CD26) in complex with… · 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 2AJ8 · PDBe 2AJ8 · UniProt P22411