Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-23
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 1-23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CY9
- Type
- protein
- Length
- 3,663 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 1-23
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1100 | 20% helix, 28% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 1-23 | protein | 121 | 5% helix, 50% 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 | 968 | 0.87 | 0.88 | 134 | empty |
| 2 | 367 | 0.82 | 0.91 | 56 | empty |
| 3 | 449 | 0.78 | 0.86 | 45 | empty |
| 4 | 416 | 0.78 | 0.87 | 57 | empty |
| 5 | 125 | 0.78 | 0.95 | 29 | empty |
Interfaces
11 interfaces between chains.
- A–C · 4520 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4376 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4347 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 896 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 877 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide (disulfide).
Compared structures
- 8CY9 · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23 · the same entry in another collection · chain B against B, 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 8CY9 · PDBe 8CY9 · UniProt P0DTC2
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