MolNFT v1 · #184829 · protein
P5C3 is a potent Fab neutralizer
7P40 · Spike glycoprotein: “P5C3 is a potent Fab neutralizer”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #184829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7P40
- Type
- protein
- Length
- 3,687 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Variable light chain P5C3 (vl); Variable heavy chain P5C3 (vh)
- UniProt
- A0A6N1BWN9
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Spike glycoprotein | protein | 998 | 22% helix, 35% strand | A0A6N1BWN9 |
| B, D, H | Variable light chain P5C3 (vl) | protein | 108 | 3% helix, 44% strand | — |
| C, F, I | Variable heavy chain P5C3 (vh) | protein | 123 | 0% 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 | 976 | 0.88 | 0.90 | 120 | empty |
| 2 | 901 | 0.86 | 0.88 | 113 | empty |
| 3 | 190 | 0.79 | 0.94 | 41 | empty |
| 4 | 304 | 0.78 | 0.89 | 40 | empty |
| 5 | 433 | 0.77 | 0.86 | 73 | empty |
Interfaces
12 interfaces between chains.
- A–G · 3865 Ų buried · 28 hydrogen bonds · protein-protein
- E–G · 3848 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 3790 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 914 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 874 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 7P40 · P5C3 is a potent fab neutralizer · 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 A0A6N1BWN9
- Elsewhere: RCSB PDB 7P40 · PDBe 7P40 · UniProt A0A6N1BWN9
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