MolNFT v1 · #191281 · protein
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-45
8CYD · Spike glycoprotein: “SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-45”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #191281 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 8CYD
- 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 2-45
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 20% 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 2-45 | protein | 121 | 8% helix, 53% 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 | 802 | 0.88 | 0.90 | 103 | empty |
| 2 | 915 | 0.86 | 0.88 | 123 | empty |
| 3 | 598 | 0.76 | 0.83 | 45 | empty |
| 4 | 367 | 0.74 | 0.85 | 44 | empty |
| 5 | 560 | 0.74 | 0.82 | 41 | empty |
Interfaces
8 interfaces between chains.
- B–C · 4271 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4225 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4163 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 826 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 803 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide (disulfide).
Compared structures
- 8CYD · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45 · 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 8CYD · PDBe 8CYD · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.