Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-8
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CYB
- Type
- protein
- Length
- 3,432 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 1-8
- UniProt
- P0DTC2
- Ligands
- AH2, NAG, BMA, MAN, FUC, GAL
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1102 | 21% helix, 31% strand | P0DTC2 |
| D | Pan-sarbecovirus nanobody 1-8 | protein | 126 | 7% helix, 47% strand | — |
Ligands and binding sites
- AH2 · 1-deoxy-alpha-D-mannopyranose · ligand
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 76 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 17 copies
- MAN · alpha-D-mannopyranose · sugar · 15 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
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 | 891 | 0.85 | 0.87 | 110 | empty |
| 2 | 647 | 0.85 | 0.90 | 73 | empty |
| 3 | 1103 | 0.84 | 0.85 | 121 | empty |
| 4 | 1092 | 0.80 | 0.81 | 97 | empty |
| 5 | 652 | 0.78 | 0.83 | 60 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4732 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4664 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4520 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 812 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 8CYB · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8 · 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 8CYB · PDBe 8CYB · UniProt P0DTC2
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