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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1111/j.1742-4658.2005.04773.x

  • 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% (includ ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
(5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NT
Query on NT

Download SDF File 
Download CCD File 
B
NETROPSIN
C18 H26 N10 O3
IDBIFFKSXLYUOT-UHFFFAOYSA-N
 Ligand Interaction
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 = 90.00
b = 38.559β = 90.00
c = 53.203γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance