Research workbench
Structural and functional impact by SARS-cov-2 omicron spike mutations
Analyse Structural and functional impact by SARS-cov-2 omicron spike mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TNW
- Type
- protein
- Length
- 3,357 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Spike glycoprotein | protein | 1119 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains C, B, A
- MAN · alpha-D-mannopyranose · sugar · 21 copies
- FUC · alpha-L-fucopyranose · 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 | 977 | 0.88 | 0.89 | 127 | empty |
| 2 | 1106 | 0.83 | 0.84 | 129 | empty |
| 3 | 199 | 0.83 | 0.96 | 29 | empty |
| 4 | 207 | 0.83 | 0.95 | 28 | empty |
| 5 | 1055 | 0.82 | 0.83 | 122 | empty |
Interfaces
3 interfaces between chains.
- C–A · 6122 Ų buried · 46 hydrogen bonds · protein-protein
- C–B · 6118 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 6117 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TNW · Structural and functional impact by SARS-CoV-2 Omicron spike mutations · 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 7TNW · PDBe 7TNW · UniProt P0DTC2
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