Research workbench
SARS-cov-2 spike (dimers) in complex with six FU2 nanobodies
Analyse SARS-cov-2 spike (dimers) in complex with six FU2 nanobodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NS6
- Type
- protein
- Length
- 7,109 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FU2 nanobody; Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, S, H, T, O, U | FU2 nanobody | protein | 133 | 8% helix, 50% strand | — |
| I | Spike GLYCOPROTEIN,FIBRITIN | protein | 1044 | 22% helix, 33% strand | P0DTC2 |
| K | Spike GLYCOPROTEIN,FIBRITIN | protein | 1062 | 21% helix, 33% strand | P0DTC2 |
| M | Spike GLYCOPROTEIN,FIBRITIN | protein | 1042 | 21% helix, 32% strand | P0DTC2 |
| J | Spike GLYCOPROTEIN,FIBRITIN | protein | 1049 | 22% helix, 33% strand | P0DTC2 |
| L | Spike GLYCOPROTEIN,FIBRITIN | protein | 1058 | 21% helix, 33% strand | P0DTC2 |
| N | Spike GLYCOPROTEIN,FIBRITIN | protein | 1056 | 21% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 copies · chains I, K, M, J, L, N
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains K
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 | 1078 | 0.87 | 0.88 | 141 | empty |
| 2 | 869 | 0.86 | 0.88 | 106 | empty |
| 3 | 721 | 0.82 | 0.86 | 70 | empty |
| 4 | 664 | 0.82 | 0.86 | 65 | empty |
| 5 | 735 | 0.78 | 0.83 | 73 | empty |
Interfaces
18 interfaces between chains.
- I–K · 4368 Ų buried · 46 hydrogen bonds · protein-protein
- J–L · 4284 Ų buried · 49 hydrogen bonds · protein-protein
- K–M · 4208 Ų buried · 40 hydrogen bonds · protein-protein
- J–N · 4193 Ų buried · 34 hydrogen bonds · protein-protein
- L–N · 4193 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 82 disulfide, 50 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7NS6 · SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies · the same entry in another collection · chain G against G, 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 7NS6 · PDBe 7NS6 · UniProt P0DTC2
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