1K2Z

The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG).

Uytterhoeven, K.Sponer, J.Van Meervelt, L.

(2002) Eur.J.Biochem. 269: 2868-2877

  • Primary Citation of Related Structures:  1JTL

  • PubMed Abstract: 
  • Single-crystal X-ray structure determinations of the complex between the minor-groove binder distamycin and d(GGCCAATTGG) reveal two 1 : 1 binding modes which differ in the orientation of the drug molecule in the minor groove. The two crystals were g ...

    Single-crystal X-ray structure determinations of the complex between the minor-groove binder distamycin and d(GGCCAATTGG) reveal two 1 : 1 binding modes which differ in the orientation of the drug molecule in the minor groove. The two crystals were grown from different crystallization conditions and found to diffract to 2.38 and 1.85 A, respectively. The structures were refined to completion using SHELXL-93, resulting in a residual R factor of 20.30% for the 2.38-A resolution structure (including 46 water molecules) and 19.74% for the 1.85-A resolution structure (including 74 water molecules). In both orientations, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and AT base pairs. With a binding site of at least five base pairs, close contacts between the terminal distamycin atoms and guanine amino groups are inevitable. The detailed nature of several of these interactions was further investigated by ab initio quantum chemical methods.


    Organizational Affiliation

    Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, 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
DMY
Query on DMY

Download SDF File 
Download CCD File 
A
DISTAMYCIN A
DISTAMYCIN; STALLIMYCIN
C22 H27 N9 O4
UPBAOYRENQEPJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 26.106α = 90.00
b = 40.928β = 90.00
c = 53.138γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
nonemodel building
SHELXL-93refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance