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(-) Description

Title :  NMR STUDY OF DEOXYRIBONUCLEIC ACID COMPLEXED WITH ACTINOMYCIN D
 
Authors :  H. Chen, X. Liu, D. J. Patel
Date :  15 Dec 95  (Deposition) - 10 Jun 96  (Release) - 27 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (5x)
NMR Structure *:  A,B,C,D  (1x)
Keywords :  Actinomycin D, Actinomycin, Anti Cancer, Antitumor, Antibiotic, Chromophore, Depsipeptide, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Chen, X. Liu, D. J. Patel
Dna Bending And Unwinding Associated With Actinomycin D Antibiotics Bound To Partially Overlapping Sites On Dna.
J. Mol. Biol. V. 258 457 1996
PubMed-ID: 8642603  |  Reference-DOI: 10.1006/JMBI.1996.0262

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*AP*GP*CP*GP*CP*TP*T)-3')
    Chains: A, B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ACTINOMYCIN D
    Chains: C, D
    Engineered: YES
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Synonym: DACTINOMYCIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
NMR Structure (5x): ABCD
NMR Structure * (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

NMR Structure (4, 14)
No.NameCountTypeFull Name
1DVA4Mod. Amino AcidD-VALINE
2MVA4Mod. Amino AcidN-METHYLVALINE
3PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR4Mod. Amino AcidSARCOSINE
NMR Structure * (4, 14)
No.NameCountTypeFull Name
1DVA4Mod. Amino AcidD-VALINE
2MVA4Mod. Amino AcidN-METHYLVALINE
3PXZ2Mod. Amino Acid2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE
4SAR4Mod. Amino AcidSARCOSINE

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:2 , DG A:3 , DC A:4 , DG B:5 , DC B:6 , DT B:7 , PRO D:9 , SAR D:10 , MVA D:11BINDING SITE FOR CHAIN C OF ACTINOMYCIN D
2AC2SOFTWAREDG A:5 , DC A:6 , DT A:7 , DA B:2 , DG B:3 , DC B:4 , PRO C:9 , SAR C:10 , MVA C:11BINDING SITE FOR CHAIN D OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FJA)

(-) Cis Peptide Bonds  (8, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5Dva C:2 -Pro C:3
21, 2, 3, 4, 5Pro C:3 -Sar C:4
31, 2, 3, 4, 5Dva C:8 -Pro C:9
41, 2, 3, 4, 5Pro C:9 -Sar C:10
51, 2, 3, 4, 5Dva D:2 -Pro D:3
61, 2, 3, 4, 5Pro D:3 -Sar D:4
71, 2, 3, 4, 5Dva D:8 -Pro D:9
81, 2, 3, 4, 5Pro D:9 -Sar D:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FJA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FJA)

(-) Exons   (0, 0)

(no "Exon" information available for 1FJA)

(-) Sequences/Alignments

NMR Structure
   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:6
                                     
                  1fja A  2 AGCGCT  7


Chain B from PDB  Type:DNA  Length:6
                                     
                  1fja B  2 AGCGCT  7


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
                  1fja C  1 TxPxxxTxPxx 11
                             | ||| |10|
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA


Chain D 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
                  1fja D  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1FJA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1FJA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FJA)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 1FJA)

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  1fja
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1FJA)

(-) 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
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