Research workbench
Crystal structure of cirv P19 bound to siRNA
Analyse Crystal structure of cirv P19 bound to siRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RPU
- Type
- protein + RNA
- Length
- 316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*C P*GP*UP*U)-3'; 19 kda protein
- UniProt
- Q66104
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*C P*GP*UP*U)-3' | rna | 21 | — | — |
| A | 19 kda protein | protein | 138 | 38% helix, 25% strand | Q66104 |
| B | 19 kda protein | protein | 136 | 36% helix, 24% strand | Q66104 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.65 | 0.75 | 46 | empty |
| 2 | 590 | 0.62 | 0.75 | 46 | empty |
| 3 | 85 | 0.51 | 0.84 | 25 | empty |
| 4 | 90 | 0.34 | 0.75 | 10 | empty |
| 5 | 55 | 0.28 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 988 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–B · 827 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 594 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 574 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–B · 534 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1RPU · Crystal Structure of CIRV p19 bound to siRNA · the same entry in another collection · chain C against C, 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 1RPU · PDBe 1RPU · UniProt Q66104
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