MolNFT v1 · #20257 · protein + RNA
Crystal structure of P19 complexed with 19-bp small interfering RNA
1R9F · 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP…: “Crystal structure of P19 complexed with 19-bp small interfering RNA”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.63). MolNFT v1 #20257 on…
- PDB
- 1R9F
- Type
- protein + RNA
- Length
- 159 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP *AP*UP*U)-3'…
- UniProt
- P11690
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP *AP*UP*U)-3' | rna | 19 | — | — |
| C | 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP *GP*UP*U)-3' | rna | 19 | — | — |
| A | Core protein P19 | protein | 121 | 38% helix, 26% strand | P11690 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.63 | 0.75 | 43 | empty |
| 2 | 117 | 0.47 | 0.80 | 25 | empty |
| 3 | 76 | 0.27 | 0.72 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 928 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–A · 465 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 446 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1R9F · Crystal structure of p19 complexed with 19-bp small interfering RNA · the same entry in another collection · chain B against B, 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 P11690
- Elsewhere: RCSB PDB 1R9F · PDBe 1R9F · UniProt P11690
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