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Structure of human SARS-cov-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region)
Analyse Structure of human SARS-cov-2 spike glycoprotein trimer bound by neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SN3
- Type
- protein
- Length
- 3,451 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Neutralizing antibody C1C-A3 heavy chain variable region…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 925 | 23% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 924 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 915 | 24% helix, 32% strand | P0DTC2 |
| D, F, H | Neutralizing antibody C1C-A3 heavy chain variable region | protein | 121 | 7% helix, 44% strand | — |
| E, G, L | Neutralizing antibody C1C-A3 light chain variable region | protein | 108 | 0% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, E, B, G, C, L
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, G, L
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 | 1110 | 0.83 | 0.84 | 122 | empty |
| 2 | 824 | 0.83 | 0.85 | 104 | empty |
| 3 | 174 | 0.79 | 0.94 | 33 | empty |
| 4 | 565 | 0.78 | 0.84 | 46 | empty |
| 5 | 619 | 0.75 | 0.81 | 44 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4477 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 4289 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4188 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 784 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 764 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 glycan, 34 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7SN3 · Structure of human SARS-CoV-2 spike glycoprotein trimer bound by 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 7SN3 · PDBe 7SN3 · UniProt P0DTC2
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