MolNFT v1 · #164612 · protein
Crystal structure nipah virus fusion glycoprotein in complex with a neutralising Fab fragment
6T3F · Fusion glycoprotein F0: “Crystal structure nipah virus fusion glycoprotein in complex with a neutralising Fab fragment”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.61). MolNFT v1 #164612 on GenesisL1: 3D…
- PDB
- 6T3F
- Type
- protein
- Length
- 870 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; FAB66 light chain; FAB66 heavy chain
- UniProt
- Q9IH63
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Fusion glycoprotein F0 | protein | 454 | 36% helix, 27% strand | Q9IH63 |
| L | FAB66 light chain | protein | 215 | 7% helix, 53% strand | — |
| H | FAB66 heavy chain | protein | 201 | 4% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains F, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.61 | 0.75 | 60 | empty |
| 2 | 136 | 0.43 | 0.75 | 20 | empty |
| 3 | 101 | 0.42 | 0.78 | 24 | empty |
| 4 | 81 | 0.39 | 0.77 | 14 | empty |
| 5 | 83 | 0.36 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1777 Ų buried · 12 hydrogen bonds · protein-protein
- F–L · 622 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 398 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6T3F · Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab… · the same entry in another collection · chain F against F, 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 6T3F · PDBe 6T3F · UniProt Q9IH63
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