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(-) Description

Title :  STRUCTURAL, PHYSICAL AND BIOLOGICAL CHARACTERISTICS OF RNA.DNA BINDING AGENT N8-ACTINOMYCIN D
 
Authors :  M. Shinomiya, W. Chu, R. G. Carlson, R. F. Weaver, F. Takusagawa
Date :  01 May 95  (Deposition) - 15 Oct 95  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Actinomycin D, Dactinomycin, Antibiotic, Anti Cancer, Antitumor, Chromophore, Depsipeptide, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kamitori, F. Takusagawa
Crystal Structure Of The 2:1 Complex Between D(Gaagcttc) An The Anticancer Drug Actinomycin D.
J. Mol. Biol. V. 225 445 1992
PubMed-ID: 1593629  |  Reference-DOI: 10.1016/0022-2836(92)90931-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
    Chains: A, B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ACTINOMYCIN D
    Chains: C
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2MVA2Mod. Amino AcidN-METHYLVALINE
3PXZ1Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR2Mod. Amino AcidSARCOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:4 , DC A:5 , DT A:6 , DT A:7 , HOH A:2009 , DA B:11 , DG B:12 , DC B:13 , DT B:14 , DT B:15 , HOH C:2001BINDING SITE FOR CHAIN C OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D55)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Dva C:2 -Pro C:3
2Pro C:3 -Sar C:4
3Dva C:8 -Pro C:9
4Pro C:9 -Sar C:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D55)

(-) Exons   (0, 0)

(no "Exon" information available for 2D55)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA  Length:8
                                       
                  2d55 A  1 GAAGCTTC  8


Chain B from PDB  Type:DNA  Length:8
                                       
                  2d55 B  9 GAAGCTTC 16


Chain C from PDB  Type:PROTEIN  Length:11
                                          
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  2d55 C  1 TxPxxxTxPxx 11
                             | ||| |10|
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2D55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D55)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2D55)

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  2d55
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

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