Research workbench
Structures of omicron spike complexes illuminate broad-spectrum neutralizing antibody development
Analyse Structures of omicron spike complexes illuminate broad-spectrum neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WS6
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 510A5 light chain; 510A5 heavy chain
- UniProt
- P0DTC2
- Pockets
- 3 · best druggability 0.58
Structure
electron microscopy · 3 distinct chains · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike protein S1 | protein | 218 | 11% helix, 23% strand | P0DTC2 |
| H | 510A5 light chain | protein | 108 | 0% helix, 44% strand | — |
| I | 510A5 heavy chain | protein | 125 | 2% helix, 44% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.58 | 0.76 | 35 | empty |
| 2 | 96 | 0.40 | 0.77 | 21 | empty |
| 3 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–I · 878 Ų buried · 8 hydrogen bonds · protein-protein
- C–I · 562 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 248 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7WS6 · Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody… · 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 7WS6 · PDBe 7WS6 · UniProt P0DTC2
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