Research workbench
Crystal structure of P domain from norovirus strain SAGA4 in complex with hbga type B (triglycan)
Analyse Crystal structure of P domain from norovirus strain SAGA4 in complex with hbga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X06
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- B5BTR7
- Ligands
- GLA, FUC
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 309 | 5% helix, 36% strand | B5BTR7 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.98 | 24 | empty |
| 2 | 244 | 0.58 | 0.79 | 31 | empty |
| 3 | 234 | 0.58 | 0.79 | 29 | empty |
| 4 | 283 | 0.58 | 0.77 | 39 | empty |
| 5 | 189 | 0.55 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1848 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4X06 · Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B… · 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 B5BTR7
- Elsewhere: RCSB PDB 4X06 · PDBe 4X06 · UniProt B5BTR7
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