Research workbench
VP8* of P[6] human rotavirus RV3
Analyse VP8* of P[6] human rotavirus RV3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VX8
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- D7F7M7
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer capsid protein VP4 | protein | 159 | 8% helix, 57% strand | D7F7M7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.37 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VX8 · VP8* of P[6] Human Rotavirus RV3 · 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 D7F7M7
- Elsewhere: RCSB PDB 5VX8 · PDBe 5VX8 · UniProt D7F7M7
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