MolNFT v1 · #144834 · RNA
Crystal structure of the mango-II fluorescent aptamer bound to TO3- biotin
6C64 · RNA (36-mer): “Crystal structure of the mango-II fluorescent aptamer bound to TO3- biotin”. X-ray diffraction, 2 ligands (EKM, K), 7 pockets (best druggability 0.71). MolNFT v1 #144834 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6C64
- 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
- EKM, 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 | — | — |
| D | RNA (32-mer) | rna | 32 | — | — |
Ligands and binding sites
- EKM · 1-methyl-4-[(1E)-3-(3-methyl-1,3-benzothiazol-3-ium-2-yl)prop-1-en-1-yl]quinolin-1-ium · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 8 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.71 | 0.82 | 25 | empty |
| 2 | 304 | 0.50 | 0.74 | 24 | EKM |
| 3 | 93 | 0.47 | 0.82 | 11 | empty |
| 4 | 219 | 0.43 | 0.73 | 16 | empty |
| 5 | 193 | 0.41 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 790 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- A–B · 228 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- A–D · 91 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 6C64 · Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-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 6C64 · PDBe 6C64
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