Research workbench
Crystal structure of RNA silencing suppressor P19 complexed with double-helical RNA 20MER PG(CUG)6C
Analyse Crystal structure of RNA silencing suppressor P19 complexed with double-helical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNX
- Type
- protein + RNA
- Length
- 288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA silencing suppressor P19; 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U…
- UniProt
- P69517
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA silencing suppressor P19 | protein | 124 | 37% helix, 26% strand | P69517 |
| B, G | 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U P*GP*C)-3' | rna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D, G, A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, 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 | 604 | 0.63 | 0.75 | 44 | MG |
| 2 | 609 | 0.63 | 0.75 | 46 | MG |
| 3 | 55 | 0.32 | 0.77 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–G · 953 Ų buried · 126 hydrogen bonds · nucleic-nucleic
- A–D · 789 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 516 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–G · 509 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–G · 419 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 4JNX · Crystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer… · 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 P69517
- Elsewhere: RCSB PDB 4JNX · PDBe 4JNX · UniProt P69517
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