Research workbench
Crystal structure of the spinach RNA aptamer in complex with dfhbi, magnesium ions
Analyse Crystal structure of the spinach RNA aptamer in complex with dfhbi, magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TS2
- Type
- RNA
- Length
- 91 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spinach aptamer RNA, bimolecular construct
- Ligands
- 38E, GLC, FRU, K, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Spinach aptamer RNA, bimolecular construct | rna | 44 | — | — |
| Y | Spinach aptamer RNA, 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 · chains Y
- FRU · beta-D-fructofuranose · sugar · chains X, Y
- K · Potassium ion · metal · 3 copies · chains X, Y
- MG · Magnesium 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 | 501 | 0.56 | 0.73 | 30 | empty |
| 2 | 263 | 0.51 | 0.76 | 19 | K |
| 3 | 214 | 0.46 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- X–Y · 2249 Ų buried · 188 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4TS2 · Crystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium 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 4TS2 · PDBe 4TS2
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