MolNFT v1 · #188397 · protein
Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-cov-2 variants
7TPR · Spike glycoprotein: “Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-cov-2 variants”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #188397 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TPR
- Type
- protein
- Length
- 4,074 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody 8A2; Nanobody 7A3
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1145 | 23% helix, 30% strand | P0DTC2 |
| D, E | Nanobody 8A2 | protein | 132 | 2% helix, 40% strand | — |
| F, G, H | Nanobody 7A3 | protein | 125 | 2% helix, 56% 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 | 1084 | 0.85 | 0.86 | 124 | empty |
| 2 | 644 | 0.83 | 0.87 | 69 | empty |
| 3 | 951 | 0.83 | 0.84 | 105 | empty |
| 4 | 436 | 0.82 | 0.90 | 50 | empty |
| 5 | 556 | 0.82 | 0.88 | 59 | empty |
Interfaces
13 interfaces between chains.
- A–B · 5912 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 5148 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 5022 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1374 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1356 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide (disulfide).
Compared structures
- 7TPR · Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants · 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 7TPR · PDBe 7TPR · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.