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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, N8-Actinomycin D, Antibiotic, Anti Cancer, Antitumor, Chromophore, Depsipeptide, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Shinomiya, W. Chu, R. G. Carlson, R. F. Weaver, F. Takusagawa
Structural, Physical, And Biological Characteristics Of Rna. Dna Binding Agent N8-Actinomycin D.
Biochemistry V. 34 8481 1995
PubMed-ID: 7541244  |  Reference-DOI: 10.1021/BI00026A032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
    ChainsA, B
    EngineeredYES
    SyntheticYES
 
Molecule 2 - N8-ACTINOMYCIN D
    ChainsC
    EngineeredYES
    Organism ScientificSTREPTOMYCES ANTIBIOTICUS
    Organism Taxid1890
    SyntheticYES

 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
3PXA1Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-3-OXO(8-AZA)PHENOXAZINE
4SAR2Mod. Amino AcidSARCOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:4 , DC A:5 , DT A:6 , DT A:7 , DA B:11 , DG B:12 , DC B:13 , HOH C:2015 , HOH C:2016 , HOH C:2018 , HOH C:2019BINDING SITE FOR CHAIN C OF N8-ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 209D)

(-) 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 209D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 209D)

(-) Exons   (0, 0)

(no "Exon" information available for 209D)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:8
                                       
                  209d A  1 GAAGCTTC  8

Chain B from PDB  Type:DNA  Length:8
                                       
                  209d 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
                  209d C  1 TxPxxxTxPxx 11
                             | ||| |10|
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXA|
                                   8-DVA
                                    10-SAR
                                     11-MVA

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  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 209D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 209D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 209D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 209D)

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  209d
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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
2d55 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
316d CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2