MolNFT v1 · #191275 · protein
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-65
8CY6 · Spike glycoprotein: “SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-65”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #191275 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 8CY6
- Type
- protein
- Length
- 3,666 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 2-65
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1100 | 22% helix, 32% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 2-65 | protein | 122 | 2% helix, 57% 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 | 639 | 0.84 | 0.89 | 83 | empty |
| 2 | 532 | 0.83 | 0.89 | 45 | empty |
| 3 | 313 | 0.76 | 0.88 | 35 | empty |
| 4 | 593 | 0.76 | 0.83 | 43 | empty |
| 5 | 603 | 0.75 | 0.82 | 42 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4199 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 4120 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 4073 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 773 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 763 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 8CY6 · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65 · 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 8CY6 · PDBe 8CY6 · UniProt P0DTC2
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