2O3Y Rna date Dec 02, 2006
title Crystal Structure Of The Homo Sapiens Cytoplasmic Ribosomal Site In Presence Of Paromamine Derivative Nb30
authors J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, T.Baasov,
compound source
Molecule: Rna (5'- R(Upupgpcpgpupcpgpcpupcpcpgpgpapapapapgp C)-3');
Chain: A, B
Engineered: Yes
 Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 21 21 2
R_factor 0.245 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.940 49.230 57.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand SPM enzyme
Primary referenceDifferential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites., Kondo J, Hainrichson M, Nudelman I, Shallom-Shezifi D, Barbieri CM, Pilch DS, Westhof E, Baasov T, Chembiochem. 2007 Sep 24;8(14):1700-1709. PMID:17705310
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (2o3y.pdb1.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 2O3Y
  • CSU: Contacts of Structural Units for 2O3Y
  • Likely Quarternary Molecular Structure file(s) for 2O3Y
  • Structure Factors (27 Kb)
  • Retrieve 2O3Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O3Y from S2C, [Save to disk]
  • Re-refined 2o3y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2O3Y 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 2O3Y
  • 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 2O3Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o3y_A] [2o3y] [2o3y_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2O3Y
  • Community annotation for 2O3Y 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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