Research workbench
Crystal structure of norovirus boxer P domain in complex with lewis Y tetrasaccharide
Analyse Crystal structure of norovirus boxer P domain in complex with lewis Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDL
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q8BCA3
- Ligands
- FUC, NDG, GAL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid | protein | 297 | 8% helix, 33% strand | Q8BCA3 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.72 | 0.98 | 17 | empty |
| 2 | 184 | 0.62 | 0.84 | 40 | empty |
| 3 | 83 | 0.56 | 0.86 | 22 | empty |
| 4 | 71 | 0.54 | 0.87 | 21 | empty |
| 5 | 146 | 0.49 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1805 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4RDL · Crystal structure of Norovirus Boxer P domain in complex with Lewis y tetrasaccharide · 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 Q8BCA3
- Elsewhere: RCSB PDB 4RDL · PDBe 4RDL · UniProt Q8BCA3
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