Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-67
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-67 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CYA
- Type
- protein
- Length
- 3,681 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 2-67
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1100 | 21% helix, 29% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 2-67 | protein | 127 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains B, A, C
- BMA · beta-D-mannopyranose · sugar · 14 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
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 | 755 | 0.88 | 0.92 | 96 | empty |
| 2 | 706 | 0.80 | 0.84 | 75 | empty |
| 3 | 460 | 0.78 | 0.86 | 55 | empty |
| 4 | 489 | 0.78 | 0.86 | 58 | empty |
| 5 | 611 | 0.77 | 0.83 | 58 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4664 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4624 Ų buried · 37 hydrogen bonds · protein-protein
- B–A · 4584 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 627 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 583 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 26 glycan (disulfide, N-glycosylation).
Compared structures
- 8CYA · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67 · the same entry in another collection · chain C against C, 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 8CYA · PDBe 8CYA · UniProt P0DTC2
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