Research workbench
Crystal structure of the spinach RNA aptamer in complex with dfhbi, barium ions
Analyse Crystal structure of the spinach RNA aptamer in complex with dfhbi, barium ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TS0
- Type
- RNA
- Length
- 91 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spinach RNA aptamer, bimolecular construct
- Ligands
- 38E, GLC, FRU, K, BA
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Spinach RNA aptamer, bimolecular construct | rna | 44 | — | — |
| Y | Spinach RNA aptamer, bimolecular construct | rna | 47 | — | — |
Ligands and binding sites
- 38E · (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one · ligand · chains X, Y
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains X, Y
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains X, Y
- K · Potassium ion · metal · 10 copies · chains X, Y
- BA · Barium ion · metal · chains X, Y
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 | 244 | 0.52 | 0.77 | 17 | K, BA |
| 2 | 362 | 0.51 | 0.73 | 28 | K |
| 3 | 196 | 0.43 | 0.74 | 18 | K |
Interfaces
1 interface between chains.
- X–Y · 2290 Ų buried · 199 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4TS0 · Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions · the same entry in another collection · chain X against X, 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 4TS0 · PDBe 4TS0
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