MolNFT v1 · #26033 · protein
Crystal structure of human dipeptidyl peptidase IV (dppiv) complex with diprotin a
1WCY: “Crystal structure of human dipeptidyl peptidase IV (dppiv) complex with diprotin a”. X-ray diffraction, 2 ligands (NAG, FUC), 15 pockets (best druggability 0.74). MolNFT v1 #26033 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1WCY
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV; Diprotin a
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- NAG, FUC
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 729 | 18% helix, 37% strand | P27487 |
| C, D | Diprotin a | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.74 | 0.98 | 22 | empty |
| 2 | 743 | 0.70 | 0.76 | 90 | empty |
| 3 | 709 | 0.70 | 0.77 | 85 | empty |
| 4 | 265 | 0.54 | 0.76 | 43 | empty |
| 5 | 203 | 0.51 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2295 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 1WCY · Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Diprotin A · 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 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 P27487
- Elsewhere: RCSB PDB 1WCY · PDBe 1WCY · UniProt P27487
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