MolNFT v1 · #143983 · protein
Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections
6BFU · Spike protein: “Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.89). MolNFT v1 #143983…
- PDB
- 6BFU
- Type
- protein
- Length
- 2,892 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein
- UniProt
- A0A140ES81
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike protein | protein | 964 | 25% helix, 34% strand | A0A140ES81 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 102 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 33 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 33 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.89 | 0.90 | 116 | empty |
| 2 | 256 | 0.83 | 0.95 | 49 | empty |
| 3 | 179 | 0.79 | 0.94 | 37 | empty |
| 4 | 112 | 0.76 | 0.96 | 24 | empty |
| 5 | 110 | 0.76 | 0.96 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6339 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 6335 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 6334 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6BFU · Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned… · the same entry in another collection · 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 A0A140ES81
- Elsewhere: RCSB PDB 6BFU · PDBe 6BFU · UniProt A0A140ES81
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