MolNFT v1 · #140866 · protein
Crystal structure of dipeptidyl peptidase IV (dpp IV) from pseudoxanthomonas mexicana WO24
5YP1 · Dipeptidyl aminopeptidase 4: “Crystal structure of dipeptidyl peptidase IV (dpp IV) from pseudoxanthomonas mexicana WO24”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #140866 on GenesisL1: 3D structure, binding…
- PDB
- 5YP1
- Type
- protein
- Length
- 2,826 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 0.86
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 695 | 16% helix, 34% strand | Q6F3I7 |
| B | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 724 | 17% helix, 35% strand | Q6F3I7 |
| C | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 704 | 17% helix, 35% strand | Q6F3I7 |
| D | Dipeptidyl aminopeptidase 4 (EC 3.4.14.5) | protein | 703 | 16% helix, 32% strand | Q6F3I7 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.86 | 0.87 | 126 | empty |
| 2 | 936 | 0.80 | 0.82 | 109 | GOL |
| 3 | 905 | 0.78 | 0.81 | 95 | empty |
| 4 | 1030 | 0.77 | 0.79 | 99 | empty |
| 5 | 957 | 0.77 | 0.79 | 111 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1580 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1433 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1318 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5YP1 · Crystal structure of dipeptidyl peptidase IV (DPP IV) from Pseudoxanthomonas mexicana WO24 · 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 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 Q6F3I7
- Elsewhere: RCSB PDB 5YP1 · PDBe 5YP1 · UniProt Q6F3I7
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