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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
- 7WS1
- Type
- protein
- Length
- 4,050 residues
- Chains
- 11
- 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 0.85
Structure
electron microscopy · 5 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1041 | 21% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1038 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1039 | 21% helix, 30% strand | P0DTC2 |
| D, H, F, J | 510A5 light chain | protein | 108 | 0% helix, 45% strand | — |
| E, I, G, K | 510A5 heavy chain | protein | 125 | 2% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, D, B, F, 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 | 639 | 0.85 | 0.89 | 82 | empty |
| 2 | 1138 | 0.84 | 0.85 | 116 | empty |
| 3 | 1093 | 0.81 | 0.82 | 96 | empty |
| 4 | 594 | 0.79 | 0.85 | 66 | empty |
| 5 | 1126 | 0.78 | 0.80 | 102 | empty |
Interfaces
17 interfaces between chains.
- A–B · 4544 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4441 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4147 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 808 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 807 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7WS1 · 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 7WS1 · PDBe 7WS1 · UniProt P0DTC2
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