Research workbench
Crystal structure of the mango-II fluorescent aptamer bound to TO1- biotin
Analyse Crystal structure of the mango-II fluorescent 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
- 6C63
- Type
- RNA
- Length
- 104 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (36-mer); RNA (32-mer)
- Ligands
- EKJ, K
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (36-mer) | rna | 36 | — | — |
| C | RNA (32-mer) | rna | 32 | — | — |
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 · 3 copies · chains A, B, C
- K · Potassium ion · metal · 8 copies · chains A, B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.71 | 0.82 | 27 | empty |
| 2 | 376 | 0.54 | 0.74 | 24 | EKJ |
| 3 | 86 | 0.45 | 0.81 | 11 | empty |
| 4 | 212 | 0.42 | 0.73 | 17 | empty |
| 5 | 190 | 0.42 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 799 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- A–B · 220 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- A–C · 94 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 6C63 · Crystal Structure of the Mango-II Fluorescent 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 6C63 · PDBe 6C63
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