MolNFT v1 · #119905 · protein
Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens
5GJ6 · Outer capsid protein VP4: “Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.74). MolNFT v1 #119905 on…
- PDB
- 5GJ6
- Type
- protein
- Length
- 1,280 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- Q9Q2P6
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Outer capsid protein VP4 | protein | 160 | 8% helix, 56% strand | Q9Q2P6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.74 | 0.84 | 45 | empty |
| 2 | 787 | 0.73 | 0.78 | 82 | SO4 |
| 3 | 485 | 0.67 | 0.79 | 63 | SO4 |
| 4 | 161 | 0.59 | 0.83 | 29 | empty |
| 5 | 272 | 0.50 | 0.74 | 34 | empty |
Interfaces
8 interfaces between chains.
- B–C · 649 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 643 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 552 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 451 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5GJ6 · Functional and structural characterization of P[19] rotavirus VP8* interaction 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 Q9Q2P6
- Elsewhere: RCSB PDB 5GJ6 · PDBe 5GJ6 · UniProt Q9Q2P6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.