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(-) Description

Title :  GENERAL STRUCTURE-BASED APPROACH TO THE DESIGN OF PROTEIN LIGANDS: APPLICATION TO THE DESIGN OF KV1.2 POTASSIUM CHANNEL BLOCKERS.
 
Authors :  C. Magis, S. Gasparini, J. B. Charbonnier, E. Stura, M. H. Le Du, A. Mene P. Cuniasse
Date :  21 Jun 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Protein Dlm1-Z-Dna Complex, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Magis, D. Gasparini, A. Lecoq, M. H. Le Du, E. Stura, J. B. Charbonnier, G. Mourier, J. C. Boulain, L. Pardo, A. Caruana, A. Joly, M. Lefranc, M. Masella, A. Menez, P. Cuniasse
Structure-Based Secondary Structure-Independent Approach To Design Protein Ligands: Application To The Design Of Kv1. 2 Potassium Channel Blockers.
J. Am. Chem. Soc. V. 128 16190 2006
PubMed-ID: 17165772  |  Reference-DOI: 10.1021/JA0646491

(-) Compounds

Molecule 1 - 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
    ChainsB, E
    EngineeredYES
    SyntheticYES
 
Molecule 2 - Z-DNA BINDING PROTEIN 1
    ChainsA, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL WINGED-HELIX DOMAIN ZALPHA
    GeneZBP1
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTUMOR STROMA AND ACTIVATED MACROPHAGE PROTEIN DLM-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2HEO)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) 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
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Chain A from PDB  Type:PROTEIN  Length:59
 aligned with ZBP1_MOUSE | Q9QY24 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:59
                                    21        31        41        51        61         
           ZBP1_MOUSE    12 DNLEQKILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSSPEPATWSIGG  70
               SCOP domains d2heoa_ A: automated matches                                SCOP domains
               CATH domains 2heoA00 A:112-170                                           CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 2heo A 112 DNLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSPSPKYWSIGG 170
                                   121       131       141       151       161         

Chain B from PDB  Type:DNA  Length:6
                                      
                 2heo B 201 CGCGCG 206

Chain D from PDB  Type:PROTEIN  Length:58
 aligned with ZBP1_MOUSE | Q9QY24 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:58
                                    21        31        41        51        61        
           ZBP1_MOUSE    12 DNLEQKILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSSPEPATWSIG  69
               SCOP domains d2heod_ D: automated matches                               SCOP domains
               CATH domains 2heoD00 D:112-169                                          CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..ee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2heo D 112 DNLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSPSPKYWSIG 169
                                   121       131       141       151       161        

Chain E from PDB  Type:DNA  Length:6
                                      
                 2heo E 201 CGCGCG 206

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (ZBP1_MOUSE | Q9QY24)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003726    double-stranded RNA adenosine deaminase activity    Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
    GO:0003692    left-handed Z-DNA binding    Interacting selectively and non-covalently with DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags.
biological process
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0060340    positive regulation of type I interferon-mediated signaling pathway    Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZBP1_MOUSE | Q9QY241j75

(-) Related Entries Specified in the PDB File

1j75 THE SAME COMPLEX, BUT WITH A MUTANT OF PROTEIN DLM1