Research workbench
Crystal structure of P[19] rotavirus VP8* complexed with LNFPI
Analyse Crystal structure of P[19] rotavirus VP8* complexed with LNFPI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VKS
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Human rotavirus A
- Molecule
- Outer capsid protein VP4
- UniProt
- A7YCM0
- Ligands
- GAL, GLC, NAG, FUC, SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.94 · 1 distinct chain · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer capsid protein VP4 | protein | 160 | 8% helix, 57% strand | A7YCM0 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 67 | 0.68 | 0.95 | 25 | empty |
| 2 | 301 | 0.56 | 0.76 | 27 | empty |
| 3 | 110 | 0.47 | 0.79 | 24 | GOL |
| 4 | 88 | 0.40 | 0.77 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 732 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5VKS · Crystal structure of P[19] rotavirus VP8* complexed with lnfpi · 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 A7YCM0
- Elsewhere: RCSB PDB 5VKS · PDBe 5VKS · UniProt A7YCM0
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