MolNFT v1 · #181336 · protein
Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain
7LRS · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody A23-58.1 that targets the…”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 13 pockets (best druggability 0.72). MolNFT v1 #181336 on…
- PDB
- 7LRS
- Type
- protein
- Length
- 625 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody A23-58.1 heavy chain; Antibody A23-58.1 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 2% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 196 | 5% helix, 19% strand | P0DTC2 |
| D | Antibody A23-58.1 heavy chain | protein | 216 | 1% helix, 36% strand | — |
| E | Antibody A23-58.1 light chain | protein | 213 | 1% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D, E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.72 | 0.90 | 38 | empty |
| 2 | 349 | 0.55 | 0.74 | 44 | empty |
| 3 | 103 | 0.49 | 0.81 | 18 | empty |
| 4 | 57 | 0.49 | 0.85 | 16 | empty |
| 5 | 140 | 0.43 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1592 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 470 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 176 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7LRS · Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that… · 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 7LRS · PDBe 7LRS · UniProt P0DTC2
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