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(-) Description

Title :  INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES
 
Authors :  A. K. Phipps, M. Tarkoy, P. Schultze, J. Feigon
Date :  05 Feb 98  (Deposition) - 06 May 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Oligonucleotide, Triplex, Propyne, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Phipps, M. Tarkoy, P. Schultze, J. Feigon
Solution Structure Of An Intramolecular Dna Triplex Containing 5-(1-Propynyl)-2'-Deoxyuridine Residues In The Third Strand.
Biochemistry V. 37 5820 1998
PubMed-ID: 9558315  |  Reference-DOI: 10.1021/BI972811U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*A)-3')
    ChainsA
    EngineeredYES
    Other DetailsHEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17. C 18, C 20, AND C 22 ARE PROTONATED
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3')
    ChainsB
    EngineeredYES
    Other DetailsHEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17. C 18, C 20, AND C 22 ARE PROTONATED
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

NMR Structure (3, 8)
No.NameCountTypeFull Name
1DC2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
2DCM1Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
3PDU5Ligand/Ion5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE

(-) Sites  (8, 8)

NMR Structure (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:1 , DC A:18BINDING SITE FOR RESIDUE PDU A 17
2AC2SOFTWAREDA A:1 , DG A:2 , DA A:3 , PDU A:17 , PDU A:19BINDING SITE FOR RESIDUE DC A 18
3AC3SOFTWAREDG A:2 , DA A:3 , DC A:18 , DCM A:20 , DC B:13BINDING SITE FOR RESIDUE PDU A 19
4AC4SOFTWAREDA A:3 , DG A:4 , DA A:5 , PDU A:19 , PDU A:21BINDING SITE FOR RESIDUE DCM A 20
5AC5SOFTWAREDA A:3 , DG A:4 , DA A:5 , DG A:6 , DCM A:20 , DC A:22 , DC B:11 , DT B:12BINDING SITE FOR RESIDUE PDU A 21
6AC6SOFTWAREDA A:5 , DG A:6 , DA A:7 , PDU A:21 , PDU A:23 , DC B:11BINDING SITE FOR RESIDUE DC A 22
7AC7SOFTWAREDG A:6 , DA A:7 , DC A:22 , PDU A:24BINDING SITE FOR RESIDUE PDU A 23
8AC8SOFTWAREDA A:7 , DA A:8 , PDU A:23BINDING SITE FOR RESIDUE PDU A 24

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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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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  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
                                       
                  1p3x A  1 AGAGAGAA  8

Chain B from PDB  Type:DNA  Length:8
                                       
                  1p3x B  9 TTCTCTCT 16

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1P3X)

(-) 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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