2DPB Dna date May 08, 2006
title Crystal Structure Of D(Cgcgaatxcgcg) Where X Is 5-(N-Aminohe Carbamoyl-2'-Deoxyuridine
authors E.C.M.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, A.Taken
compound source
Molecule: Dna (5'-D(Dcpdgpdcpdgpdapdapdtpdupdcpdg 3');
Chain: A, B
Engineered: Yes
Synthetic: Yes
Other_details: This Dna Dodecamer Is A Synthetic Construct.
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
25.539 40.833 64.456 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand CMY, K 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] (19 Kb) [Save to disk]
  • Biological Unit Coordinates (2dpb.pdb1.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 2DPB
  • CSU: Contacts of Structural Units for 2DPB
  • Likely Quarternary Molecular Structure file(s) for 2DPB
  • Structure Factors (294 Kb)
  • Retrieve 2DPB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DPB from S2C, [Save to disk]
  • Re-refined 2dpb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DPB 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 2DPB
  • 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 2DPB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dpb_A] [2dpb] [2dpb_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2DPB
  • Community annotation for 2DPB 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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