2FJV

RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine.

Goodwin, K.D.Lewis, M.A.Tanious, F.A.Tidwell, R.R.Wilson, W.D.Georgiadis, M.M.Long, E.C.

(2006) J Am Chem Soc 128: 7846-7854

  • DOI: 10.1021/ja0600936
  • Primary Citation of Related Structures:  
    2FJX, 2FJW, 2FJV

  • PubMed Abstract: 
  • A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-through ...

    A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse transcriptase A255Moloney murine leukemia virusMutation(s): 0 
Gene Names: POL
EC: 2.7.7.49 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Explore P03355 
Go to UniProtKB:  P03355
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'B8N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'G8N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      HXL
      Query on HXL

      Download Ideal Coordinates CCD File 
      G
      2-(4-(4-CARBAMIMIDOYLPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-6-CARBOXIMIDAMIDE
      C21 H18 N6 O
      CYEDCBBFAKUDNG-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.05 Å
      • R-Value Free: 0.280 
      • R-Value Work: 0.228 
      • R-Value Observed: 0.228 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 54.552α = 90
      b = 145.65β = 90
      c = 46.838γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing
      CNSrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2006-06-27
        Type: Initial release
      • Version 1.1: 2008-05-01
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance