Research workbench
Crystal structure of P domain from norovirus FUNABASHI258 stain in the complex with lewis-B
Analyse Crystal structure of P domain from norovirus FUNABASHI258 stain in the complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ASS
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q8JW44
- Ligands
- NPO, FUC, NAG, GAL, NA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 311 | 9% helix, 31% strand | Q8JW44 |
| B | Capsid protein | protein | 302 | 7% helix, 33% strand | Q8JW44 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.85 | 0.86 | 105 | empty |
| 2 | 85 | 0.74 | 0.96 | 22 | empty |
| 3 | 119 | 0.40 | 0.76 | 24 | empty |
| 4 | 71 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1782 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3ASS · Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with… · 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 Q8JW44
- Elsewhere: RCSB PDB 3ASS · PDBe 3ASS · UniProt Q8JW44
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