Research workbench
Structure of lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
Analyse Structure of lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S8H
- Type
- protein
- Length
- 1,215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G1; 18.5C Fab heavy chain; 18.5C Fab light chain; 36.1F Fab heavy chain…
- UniProt
- P08669
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G1 | protein | 186 | 30% helix, 24% strand | P08669 |
| H | 18.5C Fab heavy chain | protein | 219 | 9% helix, 51% strand | — |
| L | 18.5C Fab light chain | protein | 214 | 8% helix, 51% strand | — |
| B | 36.1F Fab heavy chain | protein | 218 | 4% helix, 50% strand | — |
| C | 36.1F Fab light chain | protein | 215 | 8% helix, 50% strand | — |
| a | Glycoprotein G2 | protein | 163 | 47% helix, 13% strand | P08669 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, a, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains a, L
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains a, L
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.70 | 0.81 | 54 | empty |
| 2 | 345 | 0.55 | 0.74 | 43 | empty |
| 3 | 107 | 0.48 | 0.80 | 18 | empty |
| 4 | 229 | 0.47 | 0.74 | 34 | empty |
| 5 | 210 | 0.45 | 0.73 | 35 | NAG |
Interfaces
9 interfaces between chains.
- A–a · 2415 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1939 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1872 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 14 hydrogen bonds · protein-protein
- H–a · 487 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7S8H · Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F · 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 P08669
- Elsewhere: RCSB PDB 7S8H · PDBe 7S8H · UniProt P08669
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