Research workbench
Structure of the mango-III fluorescent aptamer bound to YO3-biotin
Analyse Structure of the mango-III fluorescent aptamer bound to YO3-biotin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UP0
- Type
- RNA
- Length
- 76 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mango-III fluorescent aptamer
- Ligands
- YO3, MG, K
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Mango-III fluorescent aptamer | rna | 38 | — | — |
Ligands and binding sites
- YO3 · YO3-biotin · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 6 copies · chains C, D
- K · Potassium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.50 | 0.74 | 18 | empty |
| 2 | 268 | 0.48 | 0.74 | 18 | empty |
| 3 | 54 | 0.35 | 0.80 | 8 | YO3 |
| 4 | 57 | 0.33 | 0.78 | 8 | YO3 |
Compared structures
- 6UP0 · Structure of the Mango-III fluorescent aptamer bound to YO3-Biotin · the same entry in another collection · chain C against C, 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 6UP0 · PDBe 6UP0
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