1Z8V

The Structure of d(GGCCAATTGG) Complexed with Netropsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Work: 0.200 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations.

Van Hecke, K.Nam, P.C.Nguyen, M.T.Van Meervelt, L.

(2005) FEBS J 272: 3531-3541

  • DOI: https://doi.org/10.1111/j.1742-4658.2005.04773.x
  • Primary Citation of Related Structures:  
    1Z8V

  • PubMed Abstract: 

    The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.


  • Organizational Affiliation

    Biomolecular Architecture, Chemistry Department, K.U.Leuven, Heverlee, Belgium.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
(5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
A, B
10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NT
Query on NT

Download Ideal Coordinates CCD File 
C [auth B]NETROPSIN
C18 H26 N10 O3
IDBIFFKSXLYUOT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.025α = 90
b = 38.559β = 90
c = 53.203γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-14
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description