Structural, physical and biological characteristics of RNA.DNA binding agent N8-actinomycin D
DOI:10.2210/pdb2d55/pdb   NDB ID: DDH037
2D55
ENTRY 2D55 SUPERSEDES 1D55
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Dna/antibiotic
    Structure Weight: 6112.74
    Molecule: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
    Polymer: 1 Type: dna Length: 8
    Chains: A, B
    Molecule: ACTINOMYCIN D
    Polymer: 2 Type: protein Length: 11
    Chains: C
    Organism: Streptomyces antibioticus
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: 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 
    209D   CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH D(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_000001 Search  PRD_000001 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
    PXZ
    Search 
    PXZ C16 H12 N2 O4 nonPolymer
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:DDH037
     
 
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

    Previous versions:  1D55
     
  •   Revision History    Hide
    Mouse over text for details
    2012-12-12
    Other
    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
    2011-07-27
    Binding sites and description
    2011-07-27
    Non-polymer description
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.00
    R-Value: 0.190 (obs.)
    R-Free: n/a
    Space Group: C 1 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 51.37 α = 90.00 
    b = 62.09 β = 113.80 
    c = 25.04 γ = 90.00