3SKZ Rna date Jun 23, 2011
title Crystal Structure Of The 2'- Deoxyguanosine Riboswitch Bound Guanosine
authors O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov
compound source
Molecule: Rna (68-Mer)
Chain: A, B
Engineered: Yes
Other_details: Dg Riboswitch
 Synthetic: Yes
Other_details: In Vitro Transcribed Rna
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.806 47.208 227.279 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.61 Å
ligand CCC, GMP, GTP, MG, SIN, SO4 enzyme
Primary referenceStructural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch., Pikovskaya O, Polonskaia A, Patel DJ, Serganov A, Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (3skz.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (3skz.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3SKZ
  • CSU: Contacts of Structural Units for 3SKZ
  • Structure Factors (76 Kb)
  • Retrieve 3SKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SKZ from S2C, [Save to disk]
  • Re-refined 3skz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3SKZ 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 3SKZ
  • 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 3SKZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3skz_A] [3skz] [3skz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3SKZ
  • Community annotation for 3SKZ at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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