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Structural insigths into dsrna binding and RNA silencing suppression by NS3 protein of rice hoja blanca tenuivirus
Analyse Structural insigths into dsrna binding and RNA silencing suppression by NS3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AJF
- Type
- protein
- Length
- 363 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- UniProt
- Q67897
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 | protein | 92 | 63% helix, 4% strand | Q67897 |
| C | Non-structural protein 3 | protein | 89 | 65% helix, 0% strand | Q67897 |
| D | Non-structural protein 3 | protein | 90 | 67% helix, 0% strand | Q67897 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.81 | 0.83 | 81 | SO4 |
| 2 | 88 | 0.64 | 0.90 | 12 | empty |
| 3 | 62 | 0.28 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1049 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1037 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 3AJF · Structural insigths into dsRNA binding and RNA silencing suppression by NS3 protein of… · 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 Q67897
- Elsewhere: RCSB PDB 3AJF · PDBe 3AJF · UniProt Q67897
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