MolNFT v1 · #190298 · protein
Structures of omicron spike complexes illuminate broad-spectrum neutralizing antibody development
7WSA · Spike protein S1: “Structures of omicron spike complexes illuminate broad-spectrum neutralizing antibody development”. Electron microscopy, 1 ligand (NAG), 6 pockets (best druggability 0.75). MolNFT v1 #190298 on GenesisL1: 3D…
- PDB
- 7WSA
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 201 | 11% helix, 26% strand | P0DTC2 |
| D | Processed angiotensin-converting enzyme 2 | protein | 595 | 62% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.75 | 0.80 | 85 | empty |
| 2 | 268 | 0.60 | 0.79 | 32 | empty |
| 3 | 77 | 0.33 | 0.74 | 14 | empty |
| 4 | 80 | 0.31 | 0.73 | 21 | empty |
| 5 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 908 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7WSA · Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody… · the same entry in another collection · chain D against D, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.97
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7WSA · PDBe 7WSA · UniProt P0DTC2 · UniProt Q9BYF1
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