2HEO | PD0823 - JenaLib

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(TPCPGPCPGPCPG)-3'**
	Chains	:	B, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - Z-DNA BINDING PROTEIN 1
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL WINGED-HELIX DOMAIN ZALPHA
	Gene	:	ZBP1
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	TUMOR STROMA AND ACTIVATED MACROPHAGE PROTEIN DLM-1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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)
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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)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

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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