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 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/ja0600936
  • Primary Citation of Related Structures:  
    2FJV, 2FJW, 2FJX

  • 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-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse transcriptaseC [auth A]255Moloney 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)
UniProt
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Explore P03355 
Go to UniProtKB:  P03355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03355
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'A [auth B]8N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'B [auth G]8N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXL
Query on HXL
Download Ideal Coordinates CCD File 
D [auth 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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