Research workbench
Crystal structure of the prefusion glycoprotein of lcmv
Analyse Crystal structure of the prefusion glycoprotein of lcmv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5INE
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex
- UniProt
- Q9ICW1
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 348 | 35% helix, 19% strand | Q9ICW1 |
| B | Pre-glycoprotein polyprotein gp complex | protein | 339 | 34% helix, 22% strand | Q9ICW1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 11 copies
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.84 | 0.85 | 89 | empty |
| 2 | 259 | 0.69 | 0.85 | 32 | NAG |
| 3 | 245 | 0.69 | 0.85 | 32 | NAG |
| 4 | 190 | 0.57 | 0.81 | 37 | empty |
| 5 | 107 | 0.56 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2224 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 5INE · Crystal structure of the prefusion glycoprotein of LCMV · 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 Q9ICW1
- Elsewhere: RCSB PDB 5INE · PDBe 5INE · UniProt Q9ICW1
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