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(-) Description

Title :  STRUCTURE OF ACTINOMYCIN D D(ATGCGGCAT) COMPLEX
 
Authors :  Y. S. Lo, W. H. Tseng, M. H. Hou
Date :  12 Oct 12  (Deposition) - 08 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Double Helix Dna, Nucleotide Flipping-Out, Sharp Kink, Left-Handed Twist, Cgg Tripleat Repeat, Neurological Disease, Dna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. S. Lo, W. H. Tseng, C. Y. Chuang, M. H. Hou
The Structural Basis Of Actinomycin D-Binding Induces Nucleotide Flipping Out, A Sharp Bend And A Left-Handed Twist In Cgg Triplet Repeats.
Nucleic Acids Res. V. 41 4284 2013
PubMed-ID: 23408860  |  Reference-DOI: 10.1093/NAR/GKT084

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')
    ChainsA, B
    EngineeredYES
    SyntheticYES
 
Molecule 2 - ACTINOMYCIN D
    ChainsC, D
    Organism ScientificSTREPTOMYCES ANTIBIOTICUS
    Organism Taxid1890

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (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)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDT A:2 , DG A:3 , DC A:4 , DG B:14 , DG B:15 , DC B:16 , DA B:17 , DT B:18 , SAR D:4 , MVA D:5BINDING SITE FOR CHAIN C OF ACTINOMYCIN D
2AC2SOFTWAREDC A:4 , DG A:5 , DG A:6 , DC A:7 , DA A:8 , DT B:11 , DG B:12 , DC B:13 , DVA C:2 , PRO C:9 , SAR C:10BINDING SITE FOR CHAIN D OF ACTINOMYCIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HIV)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro C:3 -Sar C:4
2Pro C:9 -Sar C:10
3Dva D:2 -Pro D:3
4Pro D:3 -Sar D:4
5Dva D:8 -Pro D:9
6Pro D:9 -Sar D:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HIV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HIV)

(-) Exons   (0, 0)

(no "Exon" information available for 4HIV)

(-) 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:9
                                        
                  4hiv A  1 ATGCGGCAT  9

Chain B from PDB  Type:DNA  Length:9
                                        
                  4hiv B 10 ATGCGGCAT 18

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
                  4hiv 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
                  4hiv D  1 TxPxxxTxPxx 11
                             | ||| |10|
                             | ||| | ||
                             2-DVA | ||
                               4-SAR ||
                                5-MVA||
                                 6-PXZ|
                                   8-DVA
                                    10-SAR
                                     11-MVA

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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 4HIV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HIV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HIV)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HIV)

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