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(-) Description

Title :  MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, MOLECULAR MODELING, AND SPECTROSCOPIC STUDIES OF D(GAAGCTTC)2-ACTINOMYCIN D COMPLEXES AND ITS HOST DNA
 
Authors :  S. Kamitori, F. Takusagawa
Date :  18 Apr 94  (Deposition) - 15 Oct 94  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (2x)
Biol. Unit 2:  A,C  (2x)
Keywords :  Actinomycin, Antibiotic, Antitumor, Anticancer, Chromophore, Depsipeptide, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kamitori, F. Takusagawa
Multiple Binding Modes Of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, And Spectroscopic Studies Of D(Gaagcttc)2-Actinomycin D Complexes And Its Host Dna
J. Am. Chem. Soc. V. 116 4154 1994
PubMed: search  |  Reference-DOI: 10.1021/JA00089A002

(-) 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, D
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synonym: DACTINOMYCIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x):  B D
Biological Unit 2 (2x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2MVA2Mod. Amino AcidN-METHYLVALINE
3PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR2Mod. Amino AcidSARCOSINE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2MVA2Mod. Amino AcidN-METHYLVALINE
3PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR2Mod. Amino AcidSARCOSINE
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1DVA2Mod. Amino AcidD-VALINE
2MVA2Mod. Amino AcidN-METHYLVALINE
3PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR2Mod. Amino AcidSARCOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:4 , DC A:5 , DT A:6 , DA B:11 , HOH C:2004 , HOH C:2005 , HOH C:2006BINDING SITE FOR CHAIN C OF ACTINOMYCIN D
2AC2SOFTWAREDG B:12 , DC B:13 , DT B:14 , DT B:15 , HOH B:2025 , HOH D:2005 , HOH D:2009BINDING SITE FOR CHAIN D OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 173D)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 173D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 173D)

(-) Exons   (0, 0)

(no "Exon" information available for 173D)

(-) Sequences/Alignments

Asymmetric 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
                                       
                  173d A  1 GAAGCTTC  8


Chain B from PDB  Type:DNA  Length:8
                                       
                  173d B  9 GAAGCTTC 16


Chain C from PDB  Type:PROTEIN  Length:6
                                     
               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
                  173d C  1 TxPxxx  6
                             | |||
                             2-DVA
                               4-SAR
                                5-MVA
                                 6-PXZ


Chain D from PDB  Type:PROTEIN  Length:6
                                     
               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
                  173d D  6 xTxPxx 11
                            | | ||
                            | | ||
                            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 173D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 173D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 173D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 173D)

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  173d
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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

172d
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
2d55 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2
316d CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2