1L1V

UNUSUAL ACTD/DNA_TA COMPLEX STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Looped Out and Perpendicular: Deformation of Watson-Crick Base Pair Associated with Actinomycin D Binding.

Chou, S.H.Chin, K.H.Chen, F.M.

(2002) Proc.Natl.Acad.Sci.USA 99: 6625

  • DOI: 10.1073/pnas.102580399

  • PubMed Abstract: 
  • Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex str ...

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.


    Organizational Affiliation

    Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan 40227, Republic of China. shchou@dragon.nchu.edu.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACTINOMYCIN D
B
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*AP*CP*CP*GP*AP*C)-3'A9N/A
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000001
Query on PRD_000001
BActinomycin DPolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • 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: 2002-03-06
    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