Research workbench
Human dipeptidyl peptidase IV in complex with an alpha amino acid inhibitor
Analyse Human dipeptidyl peptidase IV in complex with an alpha amino acid inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OPH
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4 soluble form
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 277, NAG, NDG, NA
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 soluble form (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- 277 · N-(trans-4-{(1S,2S)-2-amino-3-[(3S)-3-fluoropyrrolidin-1-yl]-1-methyl-3-oxopropyl}cyclohexyl)-N-methylacetamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.76 | 0.98 | 22 | empty |
| 2 | 745 | 0.69 | 0.76 | 83 | 277 |
| 3 | 669 | 0.69 | 0.77 | 82 | 277 |
| 4 | 239 | 0.52 | 0.76 | 36 | empty |
| 5 | 226 | 0.51 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2305 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 2OPH · Human dipeptidyl peptidase IV in complex with an alpha amino acid 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 2OPH · PDBe 2OPH · UniProt P27487
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