4NYB Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine date
authors Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Amare, A.R.Ferre-D.
compound source
symmetry
R_factor
R_Free 0.2488
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.10
ligand 2QC, A23, MG, MN enzyme
Primary referenceValidating 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, Ferre-D'Amare AR, Chem Biol. 2014 May 22;21(5):591-5. doi: 10.1016/j.chembiol.2014.03.007. Epub, 2014 Apr 24. PMID:24768306
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (4nyb.pdb1.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 4NYB
  • CSU: Contacts of Structural Units for 4NYB
  • Structure Factors (52 Kb)
  • Retrieve 4NYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NYB from S2C, [Save to disk]
  • Re-refined 4nyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4NYB 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 4NYB
  • 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 4NYB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nyb_A] [4nyb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4NYB
  • Community annotation for 4NYB at PDBWiki (http://pdbwiki.org)

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