408D

STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.

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

(1998) Science 282: 111-115

  • DOI: 10.1126/science.282.5386.111
  • Primary Citation of Related Structures:  
    407D, 408D

  • PubMed Abstract: 
  • Polyamide dimers containing three types of aromatic rings-pyrrole, imidazole, and hydroxypyrrole-afford a small-molecule recognition code that discriminates among all four Watson-Crick base pairs in the minor groove. The crystal structure of a specific polyamide dimer-DNA complex establishes the structural basis for distinguishing T ...

    Polyamide dimers containing three types of aromatic rings-pyrrole, imidazole, and hydroxypyrrole-afford a small-molecule recognition code that discriminates among all four Watson-Crick base pairs in the minor groove. The crystal structure of a specific polyamide dimer-DNA complex establishes the structural basis for distinguishing T.A from A.T base pairs. Specificity for the T.A base pair is achieved by means of distinct hydrogen bonds between pairs of substituted pyrroles on the ligand and the O2 of thymine and N3 of adenine. In addition, shape-selective recognition of an asymmetric cleft between the thymine-O2 and the adenine-C2 was observed. Although hitherto similarities among the base pairs in the minor groove have been emphasized, the structure illustrates differences that allow specific minor groove recognition.


    Organizational Affiliation

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



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*GP*TP*AP*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
    IPY (Subject of Investigation/LOI)
    Query on IPY

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth B]IMIDAZOLE-PYRROLE POLYAMIDE
    C31 H42 N11 O5
    NCFLEKZHRQALKT-UHFFFAOYSA-O
     Ligand Interaction
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    IPY PDBBind:  408D Kd: 48 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.242 
    • R-Value Work: 0.219 
    • R-Value Observed: 0.219 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 60.66α = 90
    b = 30.2β = 123.59
    c = 43.46γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1998-10-19
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance