Research workbench
Crystal structure-guided design of self-assembling RNA nano triangles
Analyse Crystal structure-guided design of self-assembling RNA nano triangles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CNR
- Type
- RNA
- Length
- 54 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)- 3'); RNA…
- Ligands
- CL
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)- 3') | rna | 16 | — | — |
| B, F | RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3') | rna | 11 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.37 | 0.76 | 11 | empty |
| 2 | 53 | 0.33 | 0.78 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 502 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- E–F · 479 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 5CNR · Crystal structure-guided design of self-assembling RNA nano triangles · 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
- Elsewhere: RCSB PDB 5CNR · PDBe 5CNR
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