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A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits nipah virus and hendra virus infection
Analyse A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYS
- Type
- protein
- Length
- 2,022 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; 5B3 antibody heavy chain; 5B3 antibody light chain
- UniProt
- Q9IH63
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Fusion glycoprotein F0 | protein | 447 | 36% helix, 28% strand | Q9IH63 |
| H, C, F | 5B3 antibody heavy chain | protein | 120 | 5% helix, 48% strand | — |
| L, D, G | 5B3 antibody light chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, E
- MAN · alpha-D-mannopyranose · sugar · 12 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.78 | 0.80 | 62 | empty |
| 2 | 950 | 0.77 | 0.80 | 105 | empty |
| 3 | 1043 | 0.77 | 0.79 | 113 | empty |
| 4 | 1088 | 0.74 | 0.77 | 105 | empty |
| 5 | 1074 | 0.73 | 0.77 | 105 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2696 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 2688 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 2683 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 863 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 863 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6TYS · A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah… · the same entry in another collection · chain G against G, 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 Q9IH63
- Elsewhere: RCSB PDB 6TYS · PDBe 6TYS · UniProt Q9IH63
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