MolNFT v1 · #76135 · protein
Crystal structure of dipeptidyl peptidase IV in complex with inhibitor
3QBJ · Dipeptidyl peptidase 4: “Crystal structure of dipeptidyl peptidase IV in complex with inhibitor”. X-ray diffraction, 4 ligands (NXZ, NAG, BMA), 19 pockets (best druggability 0.72). MolNFT v1 #76135 on GenesisL1: 3D structure…
- PDB
- 3QBJ
- Type
- protein
- Length
- 1,456 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
- P27487
- Ligands
- NXZ, NAG, BMA, MAN
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- NXZ · 1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.72 | 0.76 | 115 | NXZ |
| 2 | 51 | 0.71 | 0.98 | 16 | empty |
| 3 | 614 | 0.68 | 0.77 | 82 | NXZ |
| 4 | 300 | 0.57 | 0.77 | 46 | empty |
| 5 | 462 | 0.57 | 0.73 | 58 | empty |
Interfaces
1 interface between chains.
- A–B · 2310 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3QBJ · Crystal structure of dipeptidyl peptidase IV in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · 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 P27487
- Elsewhere: RCSB PDB 3QBJ · PDBe 3QBJ · UniProt P27487
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