Research workbench
Human DPP4 in complex with ligand 34P
Analyse Human DPP4 in complex with ligand 34P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T4F
- 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
- 75M, NAG, NA
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 38% strand | P27487 |
Ligands and binding sites
- 75M · 4-({2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-4-oxo-3,4-dihydro-5H-imidazo[2,1-b]purin-5-yl}methyl) benzonitrile · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.69 | 0.76 | 83 | 75M |
| 2 | 709 | 0.68 | 0.76 | 84 | 75M |
| 3 | 413 | 0.54 | 0.73 | 47 | empty |
| 4 | 253 | 0.53 | 0.76 | 34 | empty |
| 5 | 243 | 0.53 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2307 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 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 5T4F · PDBe 5T4F · UniProt P27487
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