Research workbench
Structure of the imango-III aptamer bound to TO1-biotin
Analyse Structure of the imango-III aptamer bound to TO1-biotin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E8S
- Type
- RNA
- Length
- 76 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imango-III aptamer
- Ligands
- EKJ, SPM, NA, K, MG
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Imango-III aptamer | rna | 38 | — | — |
Ligands and binding sites
- EKJ · 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium · ligand · 2 copies · chains A, B
- SPM · Spermine · ligand · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 439 | 0.63 | 0.78 | 24 | EKJ, NA, SPM |
| 2 | 281 | 0.50 | 0.75 | 19 | MG |
| 3 | 257 | 0.48 | 0.74 | 18 | MG |
Interfaces
1 interface between chains.
- A–B · 261 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6E8S · Structure of the iMango-III aptamer bound to TO1-Biotin · 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 6E8S · PDBe 6E8S
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