1DA4

Solution structure of a DNA duplex containing the CIS-PT(NH3)2[D(-GTG-)-N7-(G)-N7(G)N7(G)]Adduct as determined with high field NMR and molecular mechanics/dynamics


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The solution structure of a DNA duplex containing the cis-Pt(NH3)2[d(-GTG-)-N7(G),N7(G)] adduct, as determined with high-field NMR and molecular mechanics/dynamics.

van Garderen, C.J.van Houte, L.P.

(1994) Eur J Biochem 225: 1169-1179

  • Primary Citation of Related Structures:  
    1DA5, 1DA4

  • PubMed Abstract: 
  • The solution structure of the cis-Pt-GTG adduct in the double-stranded oligomer d(CTCTAGTGCTCAC).td(GTGAGCACTAGAG) was studied with high-resolution NMR techniques. For model building, the distance information obtained from two-dimensional NOE experiments was used in molecular mechanic computations and molecular dynamic structure refinements ...

    The solution structure of the cis-Pt-GTG adduct in the double-stranded oligomer d(CTCTAGTGCTCAC).td(GTGAGCACTAGAG) was studied with high-resolution NMR techniques. For model building, the distance information obtained from two-dimensional NOE experiments was used in molecular mechanic computations and molecular dynamic structure refinements. The structural distortion upon platination appears to be restricted to the base pairs Pt-G6.C21 and T7.A20; Pt-G8.C19 forms a normal Watson-Crick base pair. T7 is positioned in the minor groove and stacks with the highly propeller-twisted Pt-G6. There is no hydrogen bonding between T7 and A20. The complementary strand is undistorted; A20 stacks with its flanking cytidines (C19 and C21) as in regular B-DNA. The duplex is locally unwound (from base pair A5.T22 to G8.C19: 19 degrees) and is slightly kinked (20 degrees) at the platination site. The platinum coordination distorts the DNA structure at the 5' side of the platinated-GTG-sequence and changes the minor groove face.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*TP*CP*TP*AP*GP*TP*GP*CP*TP*CP*AP*C)-3')A13N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*TP*GP*AP*GP*CP*AP*CP*TP*AP*GP*AP*G)-3')B13N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CPT (Subject of Investigation/LOI)
      Query on CPT

      Download Ideal Coordinates CCD File 
      C [auth A]Cisplatin
      Cl2 H6 N2 Pt
      LXZZYRPGZAFOLE-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Submitted: 
      • OLDERADO: 1DA4 Olderado

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1994-01-31
        Type: Initial release
      • Version 1.1: 2008-03-24
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance