1XVK

X-ray strucutre of an Echinomycin-(GCGTACGC)2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of Complexes between Echinomycin and Duplex DNA.

Cuesta-Seijo, J.A.Sheldrick, G.M.

(2005) Acta Crystallogr.,Sect.D 61: 442

  • DOI: 10.1107/S090744490500137X
  • Primary Citation of Related Structures:  1PFE, 1XVN, 1XVR

  • PubMed Abstract: 
  • The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin ...

    The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson-Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.


    Organizational Affiliation

    Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ECHINOMYCIN
B
8N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'A8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUI
Query on QUI

Download SDF File 
Download CCD File 
B
2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000491
Query on PRD_000491
BEchinomycinCyclic depsipeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.221 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 39.183α = 90.00
b = 39.183β = 90.00
c = 79.890γ = 120.00
Software Package:
Software NamePurpose
EPMRphasing
HKL-2000data reduction
SHELXL-97refinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other