MolNFT v1 · #190293 · protein
Structures of omicron spike complexes illuminate broad-spectrum neutralizing antibody development
7WS5 · Spike glycoprotein: “Structures of omicron spike complexes illuminate broad-spectrum neutralizing antibody development”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #190293 on GenesisL1: 3D…
- PDB
- 7WS5
- Type
- protein
- Length
- 3,800 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 · 4 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1035 | 22% helix, 34% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1036 | 21% helix, 34% strand | P0DTC2 |
| D, F, H | 510A5 light chain | protein | 108 | 0% helix, 41% strand | — |
| E, G, I | 510A5 heavy chain | protein | 123 | 2% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains C, B, A
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 | 706 | 0.86 | 0.90 | 72 | empty |
| 2 | 1085 | 0.86 | 0.87 | 120 | empty |
| 3 | 620 | 0.82 | 0.87 | 63 | empty |
| 4 | 770 | 0.81 | 0.84 | 74 | empty |
| 5 | 454 | 0.80 | 0.87 | 66 | empty |
Interfaces
14 interfaces between chains.
- B–C · 5033 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4681 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4249 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 846 Ų buried · 7 hydrogen bonds · protein-protein
- H–I · 822 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7WS5 · 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 7WS5 · PDBe 7WS5 · UniProt P0DTC2
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