Research workbench
Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 43E6 antibody Fab fragment
Analyse Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 43E6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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