Research workbench
Crystal structure of the E. COLI thim riboswitch bound to 1-(4- (piperazin-1-YL)PYRIDIN-3-yl)-N-(quinoxalin-6-YLMETHYL)METHANAMINE (linked compound 38)
Analyse Crystal structure of the E. COLI thim riboswitch bound to 1-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TZU
- Type
- RNA
- Length
- 79 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (79-mer)
- Ligands
- KWL, MN, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (79-mer) | rna | 79 | — | — |
Ligands and binding sites
- KWL · 1-[4-(piperazin-1-yl)pyridin-3-yl]-N-[(quinoxalin-6-yl)methyl]methanamine · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.69 | 0.78 | 40 | KWL, MG |
| 2 | 132 | 0.35 | 0.72 | 13 | empty |
| 3 | 109 | 0.33 | 0.73 | 15 | empty |
Compared structures
- 7TZU · Crystal structure of the E. coli thiM riboswitch bound to… · 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 7TZU · PDBe 7TZU
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