2DQQ Dna-Rna Hybrid date May 29, 2006
title Crystal Structure Of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- Aminohexyl)Carbamoyl-2'-O-Methyluridine
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
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Gpapapgpapapgpapg)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61
R_factor 0.246 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.471 52.471 42.488 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 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] (14 Kb) [Save to disk]
  • Biological Unit Coordinates (2dqq.pdb1.gz) 9 Kb
  • LPC: Ligand-Protein Contacts for 2DQQ
  • CSU: Contacts of Structural Units for 2DQQ
  • Likely Quarternary Molecular Structure file(s) for 2DQQ
  • Structure Factors (103 Kb)
  • Retrieve 2DQQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DQQ from S2C, [Save to disk]
  • Re-refined 2dqq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DQQ 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 2DQQ
  • 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 2DQQ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dqq] [2dqq_A] [2dqq_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2DQQ
  • Community annotation for 2DQQ 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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