Research workbench
Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody C548
Analyse Structure of the SARS-cov-2 S 6P trimer 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
- 7R8O
- Type
- protein
- Length
- 3,804 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C548 Fab heavy chain; C548 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 1034 | 23% helix, 32% strand | P0DTC2 |
| H, M, O | C548 Fab heavy chain | protein | 120 | 0% helix, 39% strand | — |
| L, N, P | C548 Fab light chain | protein | 114 | 3% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, E, M, B, O, H
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B, H
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 | 1167 | 0.87 | 0.88 | 137 | empty |
| 2 | 492 | 0.81 | 0.88 | 62 | empty |
| 3 | 763 | 0.81 | 0.84 | 91 | empty |
| 4 | 696 | 0.80 | 0.84 | 82 | empty |
| 5 | 506 | 0.80 | 0.86 | 64 | empty |
Interfaces
15 interfaces between chains.
- B–E · 5384 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 5363 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 5318 Ų buried · 44 hydrogen bonds · protein-protein
- O–P · 1025 Ų buried · 10 hydrogen bonds · protein-protein
- M–N · 1022 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 7R8O · Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C548 · 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 7R8O · PDBe 7R8O · UniProt P0DTC2
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