3OPI Dna date Sep 01, 2010
title 7-Deaza-2'-Deoxyadenosine Modification In B-Form Dna
authors E.A.Kowal, M.Ganguly, P.S.Pallan, L.A.Marky, B.Gold, M.Egli, M.P.S
compound source
Molecule: Dna (5'-D(Cpgpcpgpap(7da)Ptptpcpgpcpg
Chain: A, B
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.161 R_Free 0.195
crystal
cell
length a length b length c angle alpha angle beta angle gamma
25.635 40.310 65.928 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.10 Å
ligand 7DA, MG, NA enzyme
Primary referenceAltering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA., Kowal EA, Ganguly M, Pallan PS, Marky LA, Gold B, Egli M, Stone MP, J Phys Chem B. 2011 Dec 1;115(47):13925-34. Epub 2011 Nov 8. PMID:22059929
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (3opi.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 3OPI
  • CSU: Contacts of Structural Units for 3OPI
  • Structure Factors (294 Kb)
  • Retrieve 3OPI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OPI from S2C, [Save to disk]
  • Re-refined 3opi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3OPI 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 3OPI
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3OPI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3opi_B] [3opi] [3opi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3OPI
  • Community annotation for 3OPI at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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