Research workbench
Crystal structure of dipeptidyl peptidase IV (dpp IV) with DPP4 inhibitor from pseudoxanthomonas mexicana WO24
Analyse Crystal structure of dipeptidyl peptidase IV (dpp IV) with DPP4 inhibitor from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YP2
- Type
- protein
- Length
- 1,448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl aminopeptidase 4
- EC
- 3.4.14.5
- UniProt
- Q6F3I7
- Ligands
- 8YC
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 724 | 18% helix, 35% strand | Q6F3I7 |
Ligands and binding sites
- 8YC · (2S,5R)-1-[2-[[1-(hydroxymethyl) cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.80 | 0.82 | 116 | 8YC, GOL |
| 2 | 687 | 0.76 | 0.81 | 79 | 8YC, GOL |
| 3 | 394 | 0.74 | 0.84 | 55 | empty |
| 4 | 338 | 0.70 | 0.83 | 37 | empty |
| 5 | 340 | 0.70 | 0.83 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1224 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5YP2 · Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6F3I7 · AlphaFold monomer V2.0 prediction for dipeptidyl aminopeptidase 4 (Q6F3I7) · 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 Q6F3I7
- Elsewhere: RCSB PDB 5YP2 · PDBe 5YP2 · UniProt Q6F3I7
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