2DQP Dna-Rna Hybrid date May 29, 2006
title Structural Analyses Of Dna:Dna And Rna:Dna Duplexes Containi Aminohexyl)Carbamoyl Modified Uridines
authors E.C.M.Juan, J.Kondo, T.Ito, Y.Ueno, A.Matsuda, A.Takenaka
compound source
Molecule: Dna (5'-D(Dcp(Omu)Pdcpdtp(Omu)Pdcpdtpdtp
Chain: A
Engineered: Yes
 Synthetic: Yes
Other_details: Synthetic Constructs

Molecule: Rna (5'-R(Gpapapgpapapgpapg)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Constructs
symmetry Space Group: P 61
R_factor 0.222 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.240 52.240 42.620 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand CMY, OMU enzyme
Primary referenceCrystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules., Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A, Nucleic Acids Res. 2007 Mar 6;. PMID:17341465
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (13 Kb) [Save to disk]
  • Biological Unit Coordinates (2dqp.pdb1.gz) 9 Kb
  • LPC: Ligand-Protein Contacts for 2DQP
  • CSU: Contacts of Structural Units for 2DQP
  • Likely Quarternary Molecular Structure file(s) for 2DQP
  • Structure Factors (102 Kb)
  • Retrieve 2DQP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DQP from S2C, [Save to disk]
  • Re-refined 2dqp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DQP 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 2DQP
  • 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 2DQP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dqp_A] [2dqp_B] [2dqp]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2DQP
  • Community annotation for 2DQP 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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