Research workbench
SARS-cov-spike bound to two neutralising nanobodies
Analyse SARS-cov-spike bound to two neutralising nanobodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B18
- Type
- protein
- Length
- 3,814 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody against SARS-cov-2 vhh E; Nanobody against spike…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1011 | 21% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1012 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1041 | 21% helix, 33% strand | P0DTC2 |
| D, F, H | Nanobody against SARS-cov-2 vhh E | protein | 129 | 2% helix, 50% strand | — |
| E, G, I | Nanobody against spike glycoprotein vhh V | protein | 121 | 2% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 copies · chains C, A, B
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 | 1183 | 0.86 | 0.87 | 140 | empty |
| 2 | 379 | 0.80 | 0.89 | 66 | empty |
| 3 | 772 | 0.76 | 0.80 | 58 | empty |
| 4 | 605 | 0.75 | 0.81 | 50 | empty |
| 5 | 730 | 0.74 | 0.80 | 57 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4428 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4414 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4312 Ų buried · 40 hydrogen bonds · protein-protein
- B–G · 1066 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1057 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 37 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7B18 · SARS-CoV-spike bound to two neutralising nanobodies · 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 7B18 · PDBe 7B18 · UniProt P0DTC2
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