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(-) Description

Title :  SOLUTION STRUCTURE OF A WEDGE-SHAPED SYNTHETIC MOLECULE AT A TWO-BASE BULGE SITE IN DNA
 
Authors :  G. S. Hwang, G. B. Jones, I. H. Goldberg
Date :  09 May 03  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Wedge-Shaped Synthetic Drug-Bulged Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. S. Hwang, G. B. Jones, I. H. Goldberg
Solution Structure Of A Wedge-Shaped Synthetic Molecule At A Two-Base Bulge Site In Dna
Biochemistry V. 42 8472 2003
PubMed-ID: 12859193  |  Reference-DOI: 10.1021/BI030072D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)- 3'
    ChainsA
    EngineeredYES
    Other DetailsTHIS SEQUENCE WAS SYNTHESIZED BY DNA SYNTHESIZER.
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'
    ChainsB
    EngineeredYES
    Other DetailsTHIS SEQUENCE WAS SYNTHESIZED BY DNA SYNTHESIZER.
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1DDI1Ligand/IonSPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:6 , DG A:7 , DT A:9 , DT B:7BINDING SITE FOR RESIDUE DDI A 21

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P96)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA  Length:14
                                             
                  1p96 A  1 CACGCAGTTCGGAC 14
                                    10    

Chain B from PDB  Type:DNA  Length:12
                                           
                  1p96 B  1 GTCCGATGCGTG 12
                                    10  

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1P96)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

1kvh THE COMPLEXED STRUCTURE OF THE BULGE DNA AND NATURAL PRODUCT WITH A SIMILAR AGLYCONE STRUCTURE.