1XCS

structure of oligonucleotide/drug complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Variable role of ions in two drug intercalation complexes of DNA

Valls, N.Steiner, R.A.Wright, G.Murshudov, G.N.Subirana, J.A.

(2005) J Biol Inorg Chem 10: 476-482

  • DOI: 10.1007/s00775-005-0655-3
  • Primary Citation of Related Structures:  
    1XCS, 1XCU

  • PubMed Abstract: 
  • The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1 ...

    The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*TP*AP*CP*G)-3'A, B6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    A4L (Subject of Investigation/LOI)
    Query on A4L

    Download Ideal Coordinates CCD File 
    D [auth A]9-[(5-(ACETYLAMINO)-6-{[(1S,4R)-8-AMINO-4-[((2R)-6-AMINO-2-{2-[(1S)-5-AMINO-1-FORMYLPENTYL]HYDRAZINO}HEXANOYL)AMINO]-1-(4-AMINOBUTYL)-2,3-DIOXOOCTYL]AMINO}-6-OXOHEXYL)AMINO]-6-CHLORO-2-METHOXYACRIDINIUM
    C46 H73 Cl N11 O7
    UBQMMWHASWFFFO-QDCRQMTFSA-O
     Ligand Interaction
    BA
    Query on BA

    Download Ideal Coordinates CCD File 
    F [auth B]BARIUM ION
    Ba
    XDFCIPNJCBUZJN-UHFFFAOYSA-N
     Ligand Interaction
    CO
    Query on CO

    Download Ideal Coordinates CCD File 
    C [auth A], E [auth B]COBALT (II) ION
    Co
    XLJKHNWPARRRJB-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.40 Å
    • R-Value Free: 0.251 
    • R-Value Work: 0.193 
    • R-Value Observed: 0.199 
    • Space Group: C 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 28.659α = 90
    b = 53.473β = 90
    c = 40.691γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2005-07-19
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-11-16
      Changes: Atomic model