472D Rna date May 14, 1999
title Structure Of An Octamer Rna With Tandem Gguu Mispairs
authors J.Deng, M.Sundaralingam
compound source
Molecule: Rna (5'-R(Gpupgpupupupapc)-3')
Chain: A
Engineered: Yes
 Synthetic: Yes

Molecule: Rna (5'-R(Gpupapgpgpcpapc)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
symmetry Space Group: H 3
R_factor 0.198 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.920 41.920 56.410 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
Primary referenceSynthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs., Deng J, Sundaralingam M, Nucleic Acids Res 2000 Nov 1;28(21):4376-81. PMID:11058138
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (11 Kb) [Save to disk]
  • Biological Unit Coordinates (472d.pdb1.gz) 7 Kb
  • CSU: Contacts of Structural Units for 472D
  • Likely Quarternary Molecular Structure file(s) for 472D
  • Structure Factors (25 Kb)
  • Retrieve 472D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 472D from S2C, [Save to disk]
  • Re-refined 472d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 472D 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 472D
  • 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 472D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [472d_A] [472d_B] [472d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 472D
  • Community annotation for 472D 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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