Research workbench
Acidic omicron spike trimer
Analyse Acidic omicron spike trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WG7
- Type
- protein
- Length
- 3,313 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 20% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Spike glycoprotein | protein | 1098 | 20% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1117 | 20% helix, 23% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 68 copies · chains B, A, C
- BMA · beta-D-mannopyranose · sugar · 5 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 | 921 | 0.89 | 0.91 | 108 | empty |
| 2 | 848 | 0.87 | 0.90 | 102 | empty |
| 3 | 868 | 0.81 | 0.84 | 84 | empty |
| 4 | 591 | 0.80 | 0.86 | 83 | empty |
| 5 | 255 | 0.79 | 0.91 | 50 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5833 Ų buried · 33 hydrogen bonds · protein-protein
- B–A · 5345 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 4554 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 39 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7WG7 · Acidic Omicron Spike Trimer · the same entry in another collection · chain B against B, 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 7WG7 · PDBe 7WG7 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.