MolNFT v1 · #185278 · protein
Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 43E6 antibody Fab fragment
7PNQ · 43E6 antibody heavy chain: “Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 43E6 antibody Fab fragment”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #185278 on…
- PDB
- 7PNQ
- Type
- protein
- Length
- 4,218 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 43E6 antibody heavy chain; 43E6 antibody light chain; Spike glycoprotein
- UniProt
- Q696P8
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, H, D | 43E6 antibody heavy chain | protein | 124 | 5% helix, 44% strand | — |
| Y, L, F | 43E6 antibody light chain | protein | 107 | 3% helix, 50% strand | — |
| C, A, B | Spike glycoprotein | protein | 1175 | 21% helix, 33% strand | Q696P8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1088 | 0.87 | 0.88 | 131 | empty |
| 2 | 454 | 0.85 | 0.92 | 56 | empty |
| 3 | 690 | 0.84 | 0.88 | 73 | empty |
| 4 | 169 | 0.83 | 0.97 | 25 | empty |
| 5 | 171 | 0.83 | 0.97 | 24 | empty |
Interfaces
18 interfaces between chains.
- C–B · 6472 Ų buried · 65 hydrogen bonds · protein-protein
- C–A · 6457 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 6454 Ų buried · 65 hydrogen bonds · protein-protein
- X–Y · 897 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 895 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 69 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7PNQ · Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 43E6 antibody… · the same entry in another collection · chain X against X, 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 Q696P8
- Elsewhere: RCSB PDB 7PNQ · PDBe 7PNQ · UniProt Q696P8
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