Research workbench
Fucose-functionalized precision glycomacromolecules targeting human norovirus capsid protein
Analyse Fucose-functionalized precision glycomacromolecules targeting human norovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GY9
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Norwalk virus
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- KBA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.83 · 2 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 314 | 8% helix, 37% strand | Q5F4T5 |
| B | Capsid protein | protein | 299 | 7% helix, 35% strand | Q5F4T5 |
Ligands and binding sites
- KBA · 2-(1H-1,2,3-triazol-1-yl)ethyl 6-deoxy-alpha-L-galactopyranoside · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.75 | 0.82 | 88 | EDO |
| 2 | 158 | 0.66 | 0.86 | 25 | empty |
| 3 | 458 | 0.63 | 0.77 | 55 | empty |
| 4 | 134 | 0.48 | 0.78 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1856 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6GY9 · Fucose-functionalized precision glycomacromolecules targeting human norovirus capsid… · 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 Q5F4T5
- Elsewhere: RCSB PDB 6GY9 · PDBe 6GY9 · UniProt Q5F4T5
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