Research workbench
SARS-cov-2 S omicron spike B.1.1.529
Analyse SARS-cov-2 S omicron spike B.1.1.529 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QO7
- Type
- protein
- Length
- 3,295 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface GLYCOPROTEIN,FIBRITIN,SARS-cov-2 S omicron spike B.1.1.529
- UniProt
- A0A8A4XEV3
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface GLYCOPROTEIN,FIBRITIN,SARS-cov-2 S omicron spike B.1.1.529 | protein | 1101 | 20% helix, 25% strand | A0A8A4XEV3 |
| B | Surface GLYCOPROTEIN,FIBRITIN,SARS-cov-2 S omicron spike B.1.1.529 | protein | 1096 | 19% helix, 25% strand | A0A8A4XEV3 |
| C | Surface GLYCOPROTEIN,FIBRITIN,SARS-cov-2 S omicron spike B.1.1.529 | protein | 1098 | 20% helix, 24% strand | A0A8A4XEV3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 19 copies
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
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 | 666 | 0.87 | 0.91 | 73 | empty |
| 2 | 918 | 0.86 | 0.87 | 108 | empty |
| 3 | 1011 | 0.85 | 0.86 | 102 | empty |
| 4 | 1006 | 0.83 | 0.84 | 96 | empty |
| 5 | 1039 | 0.80 | 0.82 | 105 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5264 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 5051 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4294 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 37 glycan (disulfide, N-glycosylation).
Compared structures
- 7QO7 · SARS-CoV-2 S Omicron Spike B.1.1.529 · 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 A0A8A4XEV3
- Elsewhere: RCSB PDB 7QO7 · PDBe 7QO7 · UniProt A0A8A4XEV3
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