› 6e1t

X-ray diffraction
1.8Å resolution

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine

Released:
DOI: 10.2210/pdb6e1t/pdb
PDB entry 6e1t coloured by chain, front view.
PDB entry 6e1t coloured by chain, side view.
PDB entry 6e1t coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis
Primary publication:
Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Connelly CM, Numata T, Boer RE, Moon MH, Sinniah RS, Barchi JJ, Ferré-D'Amaré AR, Schneekloth JS
Nat Commun 10 1501 (2019)
PMID: 30940810

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197071 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
RNA (33-MER) Chain: A
Molecule details ›
Chain: A
Length: 33 nucleotides
Theoretical weight: 10.22 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MES 1 x MES
Ligand HLV 1 x HLV
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P6322
Unit cell:
a: 115.054Å b: 115.054Å c: 58.792Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.195 0.205
Expression system: Not provided

Quick links

Citations

10 review citations

Targeting RNA structures with small molecules.
Childs-Disney et al. (2022)
9 more

1 mention without citation

DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites.
Rekand et al. (2021)