1K8L

XBY6: An analog of CK14 containing 6 dithiophosphate groups


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB

Volk, D.E.Yang, X.Fennewald, S.M.King, D.J.Bassett, S.E.Venkitachalam, S.Herzog, N.Luxon, B.A.Gorenstein, D.G.

(2002) Bioorg.Chem. 30: 396-419

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experime ...

    A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.


    Organizational Affiliation

    Department of Human Biological Chemistry and Genetics, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1157, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
FIRST STRAND OF CK14 DNA DUPLEXA14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
SECOND STRAND OF CK14 DNA DUPLEXB14N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
T2S
Query on T2S
A
RNA LINKINGC10 H15 N2 O6 P S2T
G2S
Query on G2S
B
DNA LINKINGC10 H14 N5 O5 P S2DG
C2S
Query on C2S
A, B
DNA LINKINGC9 H14 N3 O5 P S2DC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance