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Structure of lassa virus glycoprotein bound to Fab 18.5C
Analyse Structure of lassa virus glycoprotein bound to Fab 18.5C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P91
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex; Fab 18.5C antibody heavy chain; Fab 18.5C…
- UniProt
- Q6GWS0
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 187 | 28% helix, 25% strand | Q6GWS0 |
| H | Fab 18.5C antibody heavy chain | protein | 218 | 6% helix, 51% strand | — |
| L | Fab 18.5C antibody light chain | protein | 214 | 5% helix, 51% strand | — |
| a | Pre-glycoprotein polyprotein gp COMPLEX,LASSA virus glycoprotein, GP2 subunit | protein | 161 | 45% helix, 14% strand | Q6GWS0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, a, L
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains a, A, L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains a, A
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.59 | 0.80 | 35 | empty |
| 2 | 392 | 0.58 | 0.75 | 47 | empty |
| 3 | 171 | 0.56 | 0.81 | 35 | NAG |
| 4 | 108 | 0.55 | 0.84 | 25 | empty |
| 5 | 50 | 0.49 | 0.87 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–a · 2534 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 1951 Ų buried · 13 hydrogen bonds · protein-protein
- H–a · 500 Ų buried · 12 hydrogen bonds · protein-protein
- L–a · 409 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 171 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6P91 · Structure of Lassa virus glycoprotein bound to Fab 18.5C · 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 Q6GWS0
- Elsewhere: RCSB PDB 6P91 · PDBe 6P91 · UniProt Q6GWS0
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