Porcine dipeptidyl peptidase IV in complex with 8-(3-aminopiperidin-1- yl)-7-[(2-BROMOPHENYL)METHYL]-1,3-dimethyl-2,3,6,7-tetrahydro-1H- purine-2,6-dione

Structure

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

Ligands and binding sites

• 6Z8 · 8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl) methyl]-1,3-dimethyl-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
• 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, 11 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 2326 Ų buried · 44 hydrogen bonds · protein-protein
• C–D · 2319 Ų buried · 40 hydrogen bonds · protein-protein
• A–C · 605 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 603 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5LLS · Porcine dipeptidyl peptidase IV 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 5LLS · PDBe 5LLS · UniProt P22411