Research workbench
Structure of the mango-III (A10U) aptamer bound to TO1-biotin
Analyse Structure of the mango-III (A10U) 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
- 6E8T
- Type
- RNA
- Length
- 143 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (35-mer)
- Ligands
- HZG, K, NA
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | RNA (35-mer) | rna | 35 | — | — |
| C, B, A | RNA (35-mer) | rna | 36 | — | — |
Ligands and binding sites
- HZG · 1-methyl-4-{[3-(2-oxopropyl)-1,3-benzothiazol-3-ium-2-yl]methyl}quinolin-1-ium · ligand · 4 copies · chains D, A, C, B
- K · Potassium ion · metal · 4 copies · chains D, C, B, A
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.64 | 0.78 | 26 | HZG |
| 2 | 464 | 0.63 | 0.78 | 28 | HZG |
| 3 | 265 | 0.51 | 0.76 | 19 | empty |
| 4 | 201 | 0.43 | 0.74 | 16 | empty |
| 5 | 148 | 0.37 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–A · 298 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–A · 294 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- C–B · 239 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6E8T · Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin · the same entry in another collection · chain D against D, 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 6E8T · PDBe 6E8T
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