Research workbench
Structure of lineage I (pinneo) lassa virus glycoprotein bound to Fab 25.10C
Analyse Structure of lineage I (pinneo) lassa virus glycoprotein bound to Fab 25.10C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UDS
- Type
- protein
- Length
- 2,094 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 25.10C Fab heavy chain; 25.10C Fab light chain; Glycoprotein G1; Glycoprotein G2
- UniProt
- Q9IMJ0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F, H | 25.10C Fab heavy chain | protein | 213 | 7% helix, 51% strand | — |
| L, G, E | 25.10C Fab light chain | protein | 209 | 7% helix, 46% strand | — |
| A, C, B | Glycoprotein G1 | protein | 137 | 31% helix, 29% strand | Q9IMJ0 |
| a, c, b | Glycoprotein G2 | protein | 139 | 46% helix, 9% strand | Q9IMJ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains F, A, a, G, H, C, L, c, D, B, E, b
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains G, F, L, H, E, D
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains G, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.76 | 0.80 | 92 | empty |
| 2 | 723 | 0.74 | 0.79 | 80 | NAG |
| 3 | 766 | 0.73 | 0.79 | 85 | NAG |
| 4 | 659 | 0.71 | 0.78 | 71 | NAG |
| 5 | 79 | 0.55 | 0.86 | 20 | empty |
Interfaces
21 interfaces between chains.
- A–a · 1954 Ų buried · 12 hydrogen bonds · protein-protein
- B–b · 1951 Ų buried · 14 hydrogen bonds · protein-protein
- C–c · 1934 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1612 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1594 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7UDS · Structure of lineage I (Pinneo) Lassa virus glycoprotein bound to Fab 25.10C · the same entry in another collection · chain D against D, 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 Q9IMJ0
- Elsewhere: RCSB PDB 7UDS · PDBe 7UDS · UniProt Q9IMJ0
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