Research workbench
Crystal structure of dipeptidyl peptidase IV in complex with tak-322
Analyse Crystal structure of dipeptidyl peptidase IV in complex with tak-322 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G0B
- Type
- protein
- Length
- 2,913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- T22, NAG
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 733 | 18% helix, 37% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 37% strand | P27487 |
Ligands and binding sites
- T22 · 2-({6-[(3R)-3-aminopiperidin-1-yl]-3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl}methyl)benzonitrile · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 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 | 54 | 0.72 | 0.99 | 21 | empty |
| 2 | 796 | 0.70 | 0.76 | 85 | T22 |
| 3 | 711 | 0.68 | 0.76 | 86 | T22 |
| 4 | 529 | 0.67 | 0.77 | 66 | T22 |
| 5 | 520 | 0.63 | 0.75 | 67 | T22 |
Interfaces
4 interfaces between chains.
- C–D · 2322 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2303 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3G0B · Crystal structure of dipeptidyl peptidase IV in complex with TAK-322 · the same entry in another collection · chain D against D, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · chain D 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 3G0B · PDBe 3G0B · UniProt P27487
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.