MolNFT v1 · #187297 · protein
Structure of lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
7S8H · Glycoprotein G1: “Structure of lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 15 pockets (best druggability 0.70). MolNFT v1 #187297 on GenesisL1: 3D structure, binding…
- 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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