› 4nyg

X-ray diffraction
3.05Å resolution

Crystal structure of the E. coli thiM riboswitch in complex with thiamine

Released:
DOI: 10.2210/pdb4nyg/pdb
PDB entry 4nyg coloured by chain, front view.
PDB entry 4nyg coloured by chain, side view.
PDB entry 4nyg 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-250420 (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 aptamer (THI element)

Ligands and Environments

2 bound ligands:
Ligand VIB 1 x VIB
Ligand MG 6 x MG
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: 61.503Å b: 61.503Å c: 103.935Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.249 0.249 0.323
Expression system: Not provided

Quick links

Citations

17 review citations

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

6 mentions without citation

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