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(-) Description

Title :  NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24
 
Authors :  D. E. Volk, X. Yang, S. M. Fennewald, D. J. King, S. E. Bassett, S. Venkitachalam, N. Herzog, B. A. Luxon, D. G. Gorenstein
Date :  24 Oct 01  (Deposition) - 15 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Phosphorodithioate, Ck14, Ck1, Nf-Kb, Xby6, Xby2, Thiophosphate, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Volk, X. Yang, S. M. Fennewald, D. J. King, S. E. Bassett, S. Venkitachalam, N. Herzog, B. A. Luxon, D. G. Gorenstein
Solution Structure And Design Of Dithiophosphate Backbone Aptamers Targeting Transcription Factor Nf-Kappab
Bioorg. Chem. V. 30 396 2002
PubMed-ID: 12642125  |  Reference-DOI: 10.1016/S0045-2068(02)00510-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIRST STRAND OF CK14 DNA DUPLEX
    Chains: A
    Engineered: YES
    Other Details: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
    Other Details - Source: SYNTHESIZED WITH NORMAL PHOSPHOROAMIDITE CHEMISTRY
    Synthetic: YES
 
Molecule 2 - SECOND STRAND OF CK14 DNA DUPLEX
    Chains: B
    Engineered: YES
    Fragment: DITHIOATED AT C22 AND C24
    Mutation: YES
    Other Details: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1
    Other Details - Source: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1C2S2Mod. NucleotideCYTIDINE-5'-DITHIOPHOSPHORATE

(-) Sites  (0, 0)

(no "Site" information available for 1K8N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K8N)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K8N)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1K8N)

(-) 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
                                             
                  1k8n A  1 CCAGGAGATTCCAC 14
                                    10    


Chain B from PDB  Type:DNA  Length:14
                                             
                  1k8n B 15 GTGGAATcTcCTGG 28
                                   |24    
                                  22-C2S  
                                    24-C2S
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1K8N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1K8N)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

1k8j NMR STRUCTURE OF CK14, THE NON-THIOATED ANALOG OF XBY6
1k8l NMR STRUCTURE OF CK14, AN ANALOG WITH 6 PHOSPHORODITHIOATES