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 PI INITIATOR PROTEIN IN COMPLEX WITH ITERON DNA
 
Authors :  M. K. Swan, D. Bastia, C. Davies
Date :  01 Nov 06  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dna Replication, Replication-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Swan, D. Bastia, C. Davies
Crystal Structure Of Pi Initiator Protein-Iteron Complex Of Plasmid R6K: Implications For Initiation Of Plasmid Dna Replication.
Proc. Natl. Acad. Sci. Usa V. 103 18481 2006
PubMed-ID: 17124167  |  Reference-DOI: 10.1073/PNAS.0609046103

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP *CP*GP*TP*CP*T)-3'
    Chains: A
    Engineered: YES
    Other Details: ITERON OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP *GP*TP*TP*CP*T)-3'
    Chains: B
    Engineered: YES
    Other Details: ITERON OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - PI PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PTXB1-INTEIN
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: PIR
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REPLICATION INITIATION PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2NRA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg C:92 -Gly C:93
2Gly C:150 -Lys C:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PIR_ECOLX_002 *P113SPIR_ECOLX  ---  ---CS113S
2UniProtVAR_PIR_ECOLX_003 *T138IPIR_ECOLX  ---  ---CT138I
3UniProtVAR_PIR_ECOLX_004 *A162SPIR_ECOLX  ---  ---CA162S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NRA)

(-) 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:DNA  Length:23
                                                       
                 2nra A   1 GAACATGAGAGCTTAGTACGTCT  23
                                    10        20   


Chain B from PDB  Type:DNA  Length:23
                                                       
                 2nra B  24 GACGTACTAAGCTCTCATGTTCT  46
                                    33        43   


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with PIR_ECOLX | P03067 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:260
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
            PIR_ECOLX     9 VNKKTKIRHRNELNHTLAQLPLPAKRVMYMALAPIDSKEPLERGRVFKIRAEDLAALAKITPSLAYRQLKEGGKLLGASKISLRGDDIIALAKELNLPFTAKNSPEELDLNIIEWIAYSPDEGYLSLKFTRTIEPYISSLIGKKNKFTTQLLTASLRLSSQYSSSLYQLIRKHYSNFKKKNYFIISVDELKEELIAYTFDKDGNIEYKYPDFPIFKRDVLNKAIAEIKKKTEISFVGFTVHEKEGRKISKLKFEFVVDED 268
               SCOP domains d2nrac1 C:9-151 Replication initiation protein PI                                                                                              d2nrac2 C:152-268 Replication initiation protein PI                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Rep_3-2nraC01 C:11-263                                                                                                                                                                                                                                       ----- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhhhhhhhhh............eeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.--------........eeeeeee....eeeeee...hhhhh.....hhh.eeeeehhhhhhh.hhhhhhhhhhhhhh.......eeeeeehhhhhhhhh.ee.......ee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------S------------------------I-----------------------S---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nra C   9 VNKKTKIRHRNELNHTLAQLPLPAKRVMYMALALIDSKEPLERGRVFKIRAEDLAALAKITPSLAYRQLKEGGKLLGASKISLRGDDIIALAKELN--------SEELDLNIIEWIAYSPDEGYLSLKFTRTIEPYISSLIGKKNKFTTQLLTASLRLSSQYSSSLYQLIRKHYSNFKKKNYFIISVDELKEELIAYTFDKDGNIEYKYPDFPIFKRDVLNKAIAEIKKKTEISFVGFTVHEKEGRKISKLKFEFVVDED 268
                                    18        28        38        48        58        68        78        88        98     |   -    |  118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
                                                                                                                         104      113
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (PIR_ECOLX | P03067)
molecular function
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

 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 2nra)
 
  Sites
(no "Sites" information available for 2nra)
 
  Cis Peptide Bonds
    Arg C:92 - Gly C:93   [ RasMol ]  
    Gly C:150 - Lys C:151   [ RasMol ]  
 

(-) 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
  2nra
    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
  PIR_ECOLX | P03067
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  PIR_ECOLX | P03067
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2NRA)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NRA)