Research workbench
Lineage I (pinneo) lassa virus glycoprotein bound to 18.5C-M30 Fab
Analyse Lineage I (pinneo) lassa virus glycoprotein bound to 18.5C-M30 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UL7
- Type
- protein
- Length
- 2,178 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G1; 18.5C-M30 Fab light chain; 18.5C-M30 Fab heavy chain; Glycoprotein G2
- UniProt
- Q9IMJ0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Glycoprotein G1 | protein | 155 | 21% helix, 28% strand | Q9IMJ0 |
| D, L, F | 18.5C-M30 Fab light chain | protein | 205 | 4% helix, 47% strand | — |
| E, H, G | 18.5C-M30 Fab heavy chain | protein | 215 | 4% helix, 47% strand | — |
| c, b, a | Glycoprotein G2 | protein | 151 | 41% helix, 16% strand | Q9IMJ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains C, c, A, a, B, b, D, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.82 | 0.86 | 84 | empty |
| 2 | 821 | 0.76 | 0.80 | 95 | empty |
| 3 | 687 | 0.73 | 0.79 | 51 | empty |
| 4 | 666 | 0.73 | 0.79 | 84 | empty |
| 5 | 321 | 0.72 | 0.85 | 34 | empty |
Interfaces
28 interfaces between chains.
- B–b · 2024 Ų buried · 17 hydrogen bonds · protein-protein
- C–c · 2002 Ų buried · 18 hydrogen bonds · protein-protein
- A–a · 1984 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1756 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 1754 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 26 glycan (disulfide, N-glycosylation).
Compared structures
- 7UL7 · Lineage I (Pinneo) Lassa virus glycoprotein bound to 18.5C-M30 Fab · the same entry in another collection · chain G against G, 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 7UL7 · PDBe 7UL7 · UniProt Q9IMJ0
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