Research workbench
Structure of a riboswitch-like RNA-ligand complex from the hepatitis C virus internal ribosome entry site
Analyse Structure of a riboswitch-like RNA-ligand complex from the hepatitis C virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZR
- Type
- RNA
- Length
- 36 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP *CP*C)-3'…
- Ligands
- SS0, MG, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP *CP*C)-3' | rna | 20 | — | — |
| B | 5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3' | rna | 16 | — | — |
Ligands and binding sites
- SS0 · (8R)-8-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine · ligand · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.45 | 0.77 | 18 | MG |
| 2 | 69 | 0.31 | 0.76 | 9 | MG, SS0 |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 77 hydrogen bonds · nucleic-nucleic
Compared structures
- 3TZR · Structure of a Riboswitch-like RNA-ligand complex from the Hepatitis C Virus Internal… · 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 3TZR · PDBe 3TZR
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.