2FJX

RT29 bound to D(CTTGAATGCATTCAAG) in complex with MMLV RT catalytic fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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
  • Structures With Same Primary Citation

  • 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-thr ...

    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: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
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)
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Go to UniProtKB:  P03355
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*GP*AP*AP*TP*G)-3'B8N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*AP*TP*TP*CP*AP*AP*G)-3'G8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXL
Query on HXL

Download CCD File 
B
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: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.749α = 90
b = 145.45β = 90
c = 46.855γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

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