MolNFT v1 · #144118 · protein + RNA
Cirv P19 protein in complex with siRNA
6BJV · RNA silencing suppressor P19: “Cirv P19 protein in complex with siRNA”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #144118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BJV
- Type
- protein + RNA
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA silencing suppressor P19; RNA (5'- R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP…
- UniProt
- Q66104
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA silencing suppressor P19 | protein | 148 | 34% helix, 22% strand | Q66104 |
| B | RNA silencing suppressor P19 | protein | 146 | 34% helix, 21% strand | Q66104 |
| C | RNA (5'- R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)- 3') | rna | 21 | — | — |
| D | RNA (5'- R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)- 3') | rna | 21 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.71 | 0.78 | 56 | empty |
| 2 | 693 | 0.66 | 0.76 | 36 | empty |
| 3 | 110 | 0.44 | 0.79 | 22 | empty |
| 4 | 86 | 0.40 | 0.78 | 16 | empty |
| 5 | 63 | 0.29 | 0.74 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 915 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–B · 798 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 523 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 511 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6BJV · CIRV p19 protein in complex with siRNA · 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 Q66104
- Elsewhere: RCSB PDB 6BJV · PDBe 6BJV · UniProt Q66104
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