Research workbench
Cryo-EM structure of bat RaTG13 spike glycoprotein
Analyse Cryo-EM structure of bat RaTG13 spike glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CN4
- Type
- protein
- Length
- 3,360 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.93
- Source
- Bat coronavirus RaTG13
- Molecule
- Spike glycoprotein
- UniProt
- A0A6B9WHD3
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 2.93 · 1 distinct chain · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1120 | 21% helix, 28% strand | A0A6B9WHD3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 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 | 1115 | 0.87 | 0.88 | 156 | empty |
| 2 | 1121 | 0.86 | 0.88 | 159 | empty |
| 3 | 816 | 0.86 | 0.89 | 120 | empty |
| 4 | 1064 | 0.86 | 0.87 | 138 | empty |
| 5 | 545 | 0.84 | 0.89 | 51 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6284 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 6271 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 6239 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 7CN4 · Cryo-EM structure of bat RATG13 spike glycoprotein · 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 7CN4 · PDBe 7CN4 · UniProt A0A6B9WHD3
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