Research workbench
Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain
Analyse Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LRT
- Type
- protein
- Length
- 4,152 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody A23-58.1 heavy chain; Antibody A23-58.1 light chain; SARS-cov-2 spike…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, H | Antibody A23-58.1 heavy chain | protein | 123 | 2% helix, 42% strand | — |
| G, L | Antibody A23-58.1 light chain | protein | 108 | 0% helix, 30% strand | — |
| D | Antibody A23-58.1 heavy chain | protein | 216 | 1% helix, 38% strand | — |
| E | Antibody A23-58.1 light chain | protein | 213 | 3% helix, 35% strand | — |
| A | SARS-cov-2 spike glycoprotein | protein | 1085 | 19% helix, 29% strand | P0DTC2 |
| B | SARS-cov-2 spike glycoprotein | protein | 1088 | 20% helix, 28% strand | P0DTC2 |
| C | SARS-cov-2 spike glycoprotein | protein | 1088 | 20% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains F, G, H, L, D, E, A, B, C
- BMA · beta-D-mannopyranose · sugar · 7 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies
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 | 900 | 0.86 | 0.88 | 100 | empty |
| 2 | 367 | 0.81 | 0.90 | 55 | empty |
| 3 | 264 | 0.76 | 0.89 | 36 | empty |
| 4 | 700 | 0.73 | 0.79 | 50 | empty |
| 5 | 196 | 0.72 | 0.89 | 28 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4295 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 4239 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 4146 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1577 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 864 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide, 49 glycan (disulfide, N-glycosylation).
Compared structures
- 7LRT · 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 7LRT · PDBe 7LRT · UniProt P0DTC2
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