3E5F Rna date Aug 13, 2008
title Crystal Structures Of The Smk Box (Sam-III) Riboswitch With
authors C.Lu
compound source
Molecule: Smk Box (Sam-III) Riboswitch For Rna
Chain: A
Engineered: Yes
 Synthetic: Yes
Other_details: The Rna Is Prepared By In Vitro Transcriptio
symmetry Space Group: I 41 2 2
R_factor 0.227 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.776 96.776 86.765 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand EEM, GTP, SR enzyme
Primary referenceCrystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism., Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A, Nat Struct Mol Biol. 2008 Oct;15(10):1076-83. Epub 2008 Sep 21. PMID:18806797
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (3e5f.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 3E5F
  • CSU: Contacts of Structural Units for 3E5F
  • Likely Quarternary Molecular Structure file(s) for 3E5F
  • Structure Factors (47 Kb)
  • Retrieve 3E5F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3E5F from S2C, [Save to disk]
  • Re-refined 3e5f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3E5F 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 3E5F
  • 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 3E5F, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3e5f] [3e5f_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3E5F
  • Community annotation for 3E5F 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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