› 4nyb

X-ray diffraction
3.1Å resolution

Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine

Released:
DOI: 10.2210/pdb4nyb/pdb
PDB entry 4nyb coloured by chain, front view.
PDB entry 4nyb coloured by chain, side view.
PDB entry 4nyb coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.
Warner KD, Homan P, Weeks KM, Smith AG, Abell C, Ferré-D'Amaré AR
Chem Biol 21 591-5 (2014)
PMID: 24768306

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195845 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
thiM TPP riboswitch Chain: A
Molecule details ›
Chain: A
Length: 83 nucleotides
Theoretical weight: 26.86 KDa
Source organism: Escherichia coli
Expression system: Not provided
Sequence domains: TPP riboswitch (THI element)

Ligands and Environments

3 bound ligands:
Ligand 2QC 1 x 2QC
Ligand MG 9 x MG
Ligand MN 4 x MN
1 modified residue:
Ligand A23 1 x A23

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P3212
Unit cell:
a: 65.243Å b: 65.243Å c: 103.269Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.188 0.249
Expression system: Not provided

Quick links

Citations

16 review citations

Principles for targeting RNA with drug-like small molecules.
Warner et al. (2018)
15 more

7 mentions without citation

Riboswitches as Drug Targets for Antibiotics.
Panchal et al. (2021)
6 more