Research workbench
Crystal structure of rat dipeptidyl peptidase (dppiv) with thiazole- based peptide mimetic #31
Analyse Crystal structure of rat dipeptidyl peptidase (dppiv) with thiazole- based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OAE
- Type
- protein
- Length
- 1,460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P14740
- Ligands
- AIL, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 730 | 19% helix, 35% strand | P14740 |
Ligands and binding sites
- AIL · N-{[(3S,5S)-5-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-3-yl]methyl}-1,3-thiazole-4-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.78 | 0.96 | 26 | empty |
| 2 | 720 | 0.69 | 0.76 | 85 | empty |
| 3 | 662 | 0.68 | 0.77 | 83 | SO4, AIL |
| 4 | 346 | 0.53 | 0.74 | 51 | empty |
| 5 | 219 | 0.52 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2205 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2OAE · Crystal structure of rat dipeptidyl peptidase (DPPIV) with thiazole-based peptide mimetic… · the same entry in another collection · chain A against A, TM-score 1.00
- P14740 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P14740) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14740
- Elsewhere: RCSB PDB 2OAE · PDBe 2OAE · UniProt P14740
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