MolNFT v1 · #106851 · RNA
Crystal structure of the spinach RNA aptamer in complex with dfhbi, magnesium ions
4TS2 · Spinach aptamer RNA, bimolecular construct: “Crystal structure of the spinach RNA aptamer in complex with dfhbi, magnesium ions”. X-ray diffraction, 5 ligands (38E, GLC, FRU), 3 pockets (best druggability 0.56). MolNFT v1 #106851 on…
- 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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