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
- 6E8U
- Type
- RNA
- Length
- 37 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (37-mer)
- Ligands
- HZD, MG, NA, K
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (37-mer) | rna | 37 | — | — |
Ligands and binding sites
- HZD · 4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains B
- NA · Sodium ion · metal · 2 copies · chains B
- K · Potassium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.52 | 0.75 | 21 | MG, NA |
| 2 | 70 | 0.38 | 0.80 | 10 | HZD |
Compared structures
- 6E8U · Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin · the same entry in another collection · chain B against B, 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 6E8U · PDBe 6E8U
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