Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH LEFT END 26-MER DNA
 
Authors :  O. Barabas, D. R. Ronning, C. Guynet, A. B. Hickman, B. Ton-Hoang, M. Chandler, F. Dyda
Date :  04 Dec 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna-Binding Protein, Protein-Dna Complex, Huh Motif, Dna Stem Loop, Transposition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Barabas, D. R. Ronning, C. Guynet, A. B. Hickman, B. Ton-Hoang, M. Chandler, F. Dyda
Mechanism Of Is200/Is605 Family Dna Transposases: Activation And Transposon-Directed Target Site Selection.
Cell(Cambridge, Mass. ) V. 132 208 2008
PubMed-ID: 18243097  |  Reference-DOI: 10.1016/J.CELL.2007.12.029

(-) Compounds

Molecule 1 - TRANSPOSASE ORFA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32B
    Fragment: RESIDUES 2-155
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: PECAN2A
    Synonym: TRANSPOSASE, IS608 TRANSPOSASE
 
Molecule 2 - 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
    Chains: C, D
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: PECAN2A
    Synonym: LEFT END 26-MER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2VIH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VIH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VIH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VIH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VIH)

(-) Exons   (0, 0)

(no "Exon" information available for 2VIH)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:151
 aligned with Q933Z0_HELPX | Q933Z0 from UniProtKB/TrEMBL  Length:155

    Alignment length:151
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 
         Q933Z0_HELPX     5 VLYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIENQQNSNRPKQKEKWKSYVDNLQTKAL 155
               SCOP domains -d2viha1 A:6-131 ISHP608 transposase                                                                                           ------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.eeeeee..hhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhhhh...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vih A   5 VLYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIENQQNSNRPKQKEKWKSYVDNLQTKAL 155
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q933Z0_HELPX | Q933Z0 from UniProtKB/TrEMBL  Length:155

    Alignment length:129
                                    14        24        34        44        54        64        74        84        94       104       114       124         
         Q933Z0_HELPX     5 VLYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIENQQN 133
               SCOP domains -d2vihb1 B:6-131 ISHP608 transposase                                                                                           -- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vih B   5 VLYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIENQQN 133
                                    14        24        34        44        54        64        74        84        94       104       114       124         


Chain C from PDB  Type:DNA  Length:25
                                                         
                 2vih C  17 AAGCCCCTAGCTTTTAGCTATGGGG  41
                                    26        36     


Chain D from PDB  Type:DNA  Length:26
                                                          
                 2vih D  16 AAAGCCCCTAGCTTTTAGCTATGGGG  41
                                    25        35
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VIH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VIH)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q933Z0_HELPX | Q933Z0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004803    transposase activity    Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
biological process
    GO:0006313    transposition, DNA-mediated    Any process involved in a type of transpositional recombination which occurs via a DNA intermediate.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2vih)
 
  Sites
(no "Sites" information available for 2vih)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vih)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2vih
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q933Z0_HELPX | Q933Z0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q933Z0_HELPX | Q933Z0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q933Z0_HELPX | Q933Z0: 2a6m 2a6o 2vhg 2vic 2vju 2vjv

(-) Related Entries Specified in the PDB File

2a6m CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE
2a6o CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEXWITH STEM-LOOP DNA
2vhg CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX WITH RIGHT END 31-MER DNA