MolNFT v1 · #105267 · protein
Bat-derived coronavirus HKU4 uses MERS-cov receptor human CD26 for cell entry
4QZV · Dipeptidyl peptidase 4: “Bat-derived coronavirus HKU4 uses MERS-cov receptor human CD26 for cell entry”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.75). MolNFT v1 #105267 on GenesisL1: 3D structure…
- PDB
- 4QZV
- Type
- protein
- Length
- 1,870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4; Spike protein S1
- EC
- 3.4.14.5
- UniProt
- P27487, A3EX94
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 37% strand | P27487 |
| B, D | Spike protein S1 | protein | 208 | 13% helix, 37% strand | A3EX94 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.75 | 0.99 | 22 | empty |
| 2 | 605 | 0.74 | 0.81 | 64 | empty |
| 3 | 559 | 0.72 | 0.80 | 66 | empty |
| 4 | 648 | 0.69 | 0.77 | 79 | empty |
| 5 | 676 | 0.68 | 0.76 | 83 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2330 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 4QZV · Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry · 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
- Every structure of UniProt A3EX94
- Elsewhere: RCSB PDB 4QZV · PDBe 4QZV · UniProt P27487 · UniProt A3EX94
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