3D2V Rna date May 09, 2008
title Structure Of The Eukaryotic Tpp-Specific Riboswitch Bound To Antibacterial Compound Pyrithiamine Pyrophosphate
authors S.Thore, C.Frick, N.Ban
compound source
Molecule: Tpp-Specific Riboswitch
Chain: A, B
Engineered: Yes
 Organism_scientific: Arabidopsis Thaliana
Expression_system: Cell-Free Synthesis
Other_details: In Vitro Transcription
symmetry Space Group: P 21 21 2
R_factor 0.207 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.790 110.780 55.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MG, PYI enzyme
Primary referenceStructural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch., Thore S, Frick C, Ban N, J Am Chem Soc. 2008 Jul 2;130(26):8116-7. Epub 2008 Jun 6. PMID:18533652
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3d2v.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (3d2v.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 3D2V
  • CSU: Contacts of Structural Units for 3D2V
  • Likely Quarternary Molecular Structure file(s) for 3D2V
  • Structure Factors (231 Kb)
  • Retrieve 3D2V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D2V from S2C, [Save to disk]
  • Re-refined 3d2v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D2V in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3D2V
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3D2V, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d2v_A] [3d2v_B] [3d2v]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3D2V
  • Community annotation for 3D2V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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