Research workbench
Prototypic SARS-cov-2 G614 spike (open form)
Analyse Prototypic SARS-cov-2 G614 spike (open form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TGX
- Type
- protein
- Length
- 3,244 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1081 | 22% helix, 30% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1082 | 21% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1081 | 21% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains C, A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains 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 | 1087 | 0.87 | 0.88 | 131 | empty |
| 2 | 948 | 0.83 | 0.84 | 67 | empty |
| 3 | 1067 | 0.82 | 0.83 | 110 | empty |
| 4 | 975 | 0.81 | 0.82 | 87 | empty |
| 5 | 684 | 0.80 | 0.85 | 77 | empty |
Interfaces
3 interfaces between chains.
- C–B · 4555 Ų buried · 31 hydrogen bonds · protein-protein
- C–A · 4514 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 4338 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7TGX · Prototypic SARS-CoV-2 G614 spike (open form) · the same entry in another collection · chain C against C, 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 P0DTC2
- Elsewhere: RCSB PDB 7TGX · PDBe 7TGX · UniProt P0DTC2
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