Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE PRECURSOR FOR CARNOBACTERIOCIN B2, AN ANTIMICROBIAL PEPTIDE FROM CARNOBACTERIUM PISCICOLA
 
Authors :  T. Sprules, K. E. Kawulka, A. C. Gibbs, D. S. Wishart, J. C. Vederas
Date :  19 Dec 03  (Deposition) - 04 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Amphipathic Helix, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Sprules, K. E. Kawulka, A. C. Gibbs, D. S. Wishart, J. C. Vederas
Nmr Solution Structure Of The Precursor For Carnobacteriocin B2, An Antimicrobial Peptide From Carnobacterium Piscicola.
Eur. J. Biochem. V. 271 1748 2004
PubMed-ID: 15096213  |  Reference-DOI: 10.1111/J.1432-1033.2004.04085.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOCIN CARNOBACTERIOCIN B2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMAL-C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCBNB2, CANCP52
    Organism ScientificCARNOBACTERIUM MALTAROMATICUM
    Organism Taxid2751
    StrainLV17B
    SynonymCARNOCIN CP52

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RY3)

(-) Sites  (0, 0)

(no "Site" information available for 1RY3)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:9 -A:14

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RY3)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIOCIN_IIAPS60030 Bacteriocin class IIa family signature.CBB2_CARML21-32  1A:3-14

(-) Exons   (0, 0)

(no "Exon" information available for 1RY3)

(-) Sequences/Alignments

NMR Structure
   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:64
 aligned with CBB2_CARML | P38580 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:64
                                    10        20        30        40        50        60    
           CBB2_CARML     1 MNSVKELNVKEMKQLHGGVNYGNGVSCSKTKCSVNWGQAFQERYTAGINSFVSGVASGAGSIGR  64
               SCOP domains d1ry3a_ A: Carnobacteriocin B2                                   SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ------------------Bacteriocin_II-1ry3A01 A:1-36       ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------BACTERIOCIN_-------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1ry3 A -18 MNSVKELNVKEMKQLHGGVNYGNGVSCSKTKCSVNWGQAFQERYTAGINSFVSGVASGAGSIGR  46
                                    -9       ||2        12        22        32        42    
                                            -1|                                             
                                              1                                             

   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, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RY3)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (CBB2_CARML | P38580)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

NMR Structure
  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 1ry3)
 
  Sites
(no "Sites" information available for 1ry3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ry3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ry3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CBB2_CARML | P38580
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CBB2_CARML | P38580
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CBB2_CARML | P385801cw5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RY3)