Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-34
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-34 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CYC
- Type
- protein
- Length
- 3,677 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 2-34
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1097 | 20% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1102 | 22% helix, 29% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 2-34 | protein | 127 | 10% helix, 46% 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 | 959 | 0.85 | 0.86 | 107 | empty |
| 2 | 949 | 0.83 | 0.85 | 96 | empty |
| 3 | 494 | 0.83 | 0.89 | 48 | empty |
| 4 | 125 | 0.77 | 0.95 | 34 | empty |
| 5 | 396 | 0.77 | 0.87 | 47 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4550 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4470 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4410 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 932 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 927 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide (disulfide).
Compared structures
- 8CYC · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 · 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 8CYC · PDBe 8CYC · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.