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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
- 7WS0
- Type
- protein
- Length
- 3,817 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 510A5 light chain; 510A5 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1041 | 21% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1038 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1039 | 21% helix, 28% strand | P0DTC2 |
| D, F, H | 510A5 light chain | protein | 108 | 0% helix, 43% strand | — |
| E, G, I | 510A5 heavy chain | protein | 125 | 7% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, D, B, 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 | 945 | 0.86 | 0.87 | 88 | empty |
| 2 | 694 | 0.84 | 0.88 | 89 | empty |
| 3 | 765 | 0.82 | 0.85 | 72 | empty |
| 4 | 816 | 0.81 | 0.84 | 94 | empty |
| 5 | 772 | 0.80 | 0.83 | 73 | empty |
Interfaces
18 interfaces between chains.
- A–C · 4493 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4473 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 4342 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 814 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 811 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7WS0 · Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody… · 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 7WS0 · PDBe 7WS0 · UniProt P0DTC2
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