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Structural, physical and biological characteristics of RNA:DNA binding agent N8-actinomycin D
DOI:10.2210/pdb209d/pdb   NDB ID: DDH051
209D
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Dna/antibiotic
    Structure Weight: 6113.73
    Molecule: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
    Polymer: 1 Type: dna Length: 8
    Chains: A, B
    Molecule: N8-ACTINOMYCIN D
    Polymer: 2 Type: protein Length: 11
    Chains: C
    Organism Streptomyces antibioticus
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct (Streptomyces antibioticus)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    173D  CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 
    1A7Y  CRYSTAL STRUCTURE OF ACTINOMYCIN D 
    1A7Z  CRYSTAL STRUCTURE OF ACTINOMYCIN Z3 
    1DSC  SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 
    1DSD  SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GATGCTTC)2 
    1FJA  SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (AAGCGCTT)2 
    1I3W  CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CGATCGATCG)2 
    1L1V  SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH MISMATCHED DNA (GTCACCGAC) 
    1MNV  CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (ATGCTGCAT)2 
    1OVF  SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CCGTTTTGTGG)2 
    1QFI  CRYSTAL STRUCTURE OF ACTINOMYCIN X2 
    1UNJ  CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A NON-COMPLEMENTARY DNA (TTAGT)2 
    1UNM  CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH NON-COMPLEMENTARY DNA 
    2D55  CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 
    316D  CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 
     
  •   Biologically Interesting Molecules (BIRD) Hide
    Identifier Image Name Type Class Chain ID  
    PRD_000011 Search  PRD_000011 N8-Actinomycin D Polypeptide Antibiotic C
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    DVA
    Search 
    DVA C5 H11 N O2 dPeptideLinking
    SAR
    Search 
    SAR C3 H7 N O2 GLY glycine
    MVA
    Search 
    MVA C6 H13 N O2 VAL lPeptideLinking
    PXA
    Search 
    PXA C15 H11 N3 O4 nonPolymer
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: DDH051
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Shinomiya, M.,  Chu, W.,  Carlson, R.G.,  Weaver, R.F.,  Takusagawa, F.

    Deposition:   1995-05-01
    Release:   1995-10-15
    Last Modified (REVDAT):   2011-07-27
     
  •   Revision History    Hide
    Mouse over text for details
    2012-12-12
    Other
    2011-07-27
    Binding sites and description
    2011-07-27
    Non-polymer description
    2011-07-27
    Function and keywords
    2011-07-27
    Linkage
    2011-07-27
    Sequence database correspondence
    2011-07-27
    Polymer description
    2011-07-27
    Atom nomenclature
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
    N/A
    Resolution[Å]:   3.00
    R-Value: 0.173 (obs.)
    R-Free: n/a
    Space Group: P 31 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 62.30 α = 90.00 
    b = 62.30 β = 90.00 
    c = 42.97 γ = 120.00