Research workbench
SARS-cov-2 S protein S:A222V + S:D614G mutant 1-up
Analyse SARS-cov-2 S protein S:A222V + S:D614G mutant 1-up in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QDG
- Type
- protein
- Length
- 3,193 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P0DTC2
- Ligands
- NAG, NDG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 1070 | 21% helix, 28% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1049 | 20% helix, 27% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1074 | 22% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains A, C, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 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 | 1141 | 0.83 | 0.84 | 107 | empty |
| 2 | 708 | 0.83 | 0.87 | 72 | empty |
| 3 | 628 | 0.82 | 0.87 | 80 | empty |
| 4 | 1168 | 0.81 | 0.82 | 106 | empty |
| 5 | 1078 | 0.80 | 0.81 | 93 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5208 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4991 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 4741 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 35 glycan (disulfide, N-glycosylation).
Compared structures
- 7QDG · SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up · 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 P0DTC2
- Elsewhere: RCSB PDB 7QDG · PDBe 7QDG · UniProt P0DTC2
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