Research workbench
Ispinach aptamer
Analyse Ispinach aptamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OB3
- Type
- RNA
- Length
- 69 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA aptamer (69-mer)
- Ligands
- 1TU, SPM, K
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA aptamer (69-mer) | rna | 69 | — | — |
Ligands and binding sites
- 1TU · 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol · ligand · chains A
- SPM · Spermine · ligand · chains A
- K · Potassium ion · metal · 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 | 506 | 0.57 | 0.74 | 29 | empty |
| 2 | 130 | 0.44 | 0.78 | 16 | 1TU |
| 3 | 142 | 0.37 | 0.73 | 14 | empty |
Compared structures
- 5OB3 · iSpinach aptamer · 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 5OB3 · PDBe 5OB3
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