1CVX

CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.

Kielkopf, C.L.Bremer, R.E.White, S.Szewczyk, J.W.Turner, J.M.Baird, E.E.Dervan, P.B.Rees, D.C.

(2000) J Mol Biol 295: 557-567

  • DOI: 10.1006/jmbi.1999.3364
  • Primary Citation of Related Structures:  
    1CVX, 1CVY

  • PubMed Abstract: 
  • Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished ...

    Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.


    Organizational Affiliation

    Division of Chemistry, California Institute of Technology, Pasadena, CA, 91125, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'A, B10N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    HP2 (Subject of Investigation/LOI)
    Query on HP2

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth B]HYDROXYPYRROLE-IMIDAZOLE-PYRROLE POLYAMIDE
    C31 H41 N11 O6
    WNWMZSNXDXZKBO-UHFFFAOYSA-N
     Ligand Interaction
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    HP2 PDBBind:  1CVX Kd: 1.10e+4 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.27 Å
    • R-Value Free: 0.238 
    • R-Value Work: 0.237 
    • R-Value Observed: 0.237 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 34.2α = 90
    b = 34.2β = 90
    c = 46.1γ = 120
    Software Package:
    Software NamePurpose
    AMoREphasing
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-01-15
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance