Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-22
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CXQ
- Type
- protein
- Length
- 3,666 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 1-22
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1100 | 21% helix, 30% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 1-22 | protein | 122 | 2% helix, 54% strand | — |
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 | 771 | 0.85 | 0.88 | 100 | empty |
| 2 | 706 | 0.85 | 0.89 | 84 | empty |
| 3 | 1153 | 0.83 | 0.84 | 119 | empty |
| 4 | 468 | 0.73 | 0.82 | 41 | empty |
| 5 | 494 | 0.71 | 0.81 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4459 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4289 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4228 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 739 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 734 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 8CXQ · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22 · 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 8CXQ · PDBe 8CXQ · UniProt P0DTC2
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