2HOO Rna date Jul 14, 2006
title Crystal Structure Of An E. Coli Thi-Box Riboswitch Bound To Benfotiamine
authors T.E.Edwards, A.R.Ferre-D'Amare
compound source
Molecule: Thi-Box Riboswitch
Chain: A
Engineered: Yes
 Synthetic: Yes
Other_details: In Vitro T7 Rna Polymerase With 5'Cis-Hammer Ribozyme And 5'-Trans Vs Ribozyme
symmetry Space Group: P 32 1 2
R_factor 0.212 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.400 61.400 102.900 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand BFT, CA enzyme
Primary referenceCrystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition., Edwards TE, Ferre-D'Amare AR, Structure. 2006 Sep;14(9):1459-68. PMID:16962976
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (2hoo.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 2HOO
  • CSU: Contacts of Structural Units for 2HOO
  • Likely Quarternary Molecular Structure file(s) for 2HOO
  • Structure Factors (36 Kb)
  • Retrieve 2HOO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HOO from S2C, [Save to disk]
  • Re-refined 2hoo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2HOO 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 2HOO
  • 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 2HOO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hoo_A] [2hoo]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2HOO
  • Community annotation for 2HOO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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