MolNFT v1 · #171779 · protein
Spike protein of RATG13 bat coronavirus in closed conformation
6ZGF · Spike glycoprotein: “Spike protein of RATG13 bat coronavirus in closed conformation”. Electron microscopy, 3 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #171779 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ZGF
- Type
- protein
- Length
- 3,180 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A6B9WHD3
- Ligands
- NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1060 | 20% helix, 32% strand | A0A6B9WHD3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 1019 | 0.85 | 0.86 | 122 | empty |
| 2 | 1028 | 0.85 | 0.86 | 121 | empty |
| 3 | 936 | 0.85 | 0.86 | 112 | empty |
| 4 | 764 | 0.85 | 0.88 | 71 | empty |
| 5 | 1112 | 0.84 | 0.85 | 125 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5613 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 5609 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 5595 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZGF · Spike Protein of RaTG13 Bat Coronavirus in Closed Conformation · 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 A0A6B9WHD3
- Elsewhere: RCSB PDB 6ZGF · PDBe 6ZGF · UniProt A0A6B9WHD3
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