MolNFT v1 · #188598 · RNA
Crystal structure of the E. COLI thim riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17)
7TZS · RNA (80-mer): “Crystal structure of the E. COLI thim riboswitch in complex with quinoxalin-6-ylmethanamine (compound 17)”. X-ray diffraction, 4 ligands (KX3, MG, K), 8 pockets (best druggability 0.66). MolNFT v1 #188598 on…
- PDB
- 7TZS
- Type
- RNA
- Length
- 160 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (80-mer)
- Ligands
- KX3, MG, K, NA
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | RNA (80-mer) | rna | 80 | — | — |
Ligands and binding sites
- KX3 · 1-(quinoxalin-6-yl)methanamine · ligand · 2 copies · chains X, Y
- MG · Magnesium ion · metal · 5 copies · chains X, Y
- K · Potassium ion · metal · 5 copies · chains X, Y
- NA · Sodium ion · metal · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.66 | 0.79 | 29 | KX3, MG |
| 2 | 502 | 0.66 | 0.79 | 31 | KX3, MG |
| 3 | 156 | 0.49 | 0.79 | 17 | K |
| 4 | 166 | 0.45 | 0.76 | 16 | K |
| 5 | 165 | 0.43 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- X–Y · 163 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7TZS · Crystal structure of the E. coli thiM riboswitch in complex with… · the same entry in another collection · chain X against X, 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 7TZS · PDBe 7TZS
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