MolNFT v1 · #144835 · RNA
Crystal structure of the mango-II-A22U fluorescent aptamer bound to TO1-biotin
6C65 · RNA (36-mer): “Crystal structure of the mango-II-A22U fluorescent aptamer bound to TO1-biotin”. X-ray diffraction, 2 ligands (EKJ, K), 6 pockets (best druggability 0.71). MolNFT v1 #144835 on GenesisL1: 3D structure, binding sites…
- PDB
- 6C65
- Type
- RNA
- Length
- 106 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (36-mer); RNA (35-mer)
- Ligands
- EKJ, K
- Pockets
- 6 · 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 (35-mer) | rna | 34 | — | — |
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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.71 | 0.80 | 35 | EKJ |
| 2 | 375 | 0.53 | 0.74 | 23 | EKJ |
| 3 | 288 | 0.48 | 0.74 | 17 | empty |
| 4 | 284 | 0.48 | 0.74 | 21 | empty |
| 5 | 77 | 0.44 | 0.82 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 815 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- A–B · 215 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–C · 92 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 6C65 · Crystal Structure of the Mango-II-A22U 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 6C65 · PDBe 6C65
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