MolNFT v1 · #140869 · protein
Crystal structure of dipeptidyl peptidase IV (dpp IV) with lys-pro from pseudoxanthomonas mexicana WO24
5YP4 · Dipeptidyl aminopeptidase 4: “Crystal structure of dipeptidyl peptidase IV (dpp IV) with lys-pro from pseudoxanthomonas mexicana WO24”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #140869 on GenesisL1: 3D…
- PDB
- 5YP4
- Type
- protein
- Length
- 2,857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl aminopeptidase 4
- EC
- 3.4.14.5
- UniProt
- Q6F3I7
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 726 | 18% helix, 35% strand | Q6F3I7 |
| C | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 689 | 17% helix, 36% strand | Q6F3I7 |
| D | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 716 | 18% helix, 35% strand | Q6F3I7 |
Ligands and binding sites
- GOL · Glycerol · additive · 21 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.79 | 0.82 | 78 | empty |
| 2 | 983 | 0.78 | 0.80 | 106 | GOL |
| 3 | 1121 | 0.77 | 0.79 | 95 | GOL |
| 4 | 847 | 0.75 | 0.79 | 75 | GOL |
| 5 | 837 | 0.75 | 0.79 | 76 | GOL |
Interfaces
4 interfaces between chains.
- C–D · 1201 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1178 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 729 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YP4 · Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pro from Pseudoxanthomonas… · the same entry in another collection · chain D against D, 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 5YP4 · PDBe 5YP4 · UniProt Q6F3I7
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