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 :  COBATOXIN 1 FROM CENTRUROIDES NOXIUS SCORPION VENOM: CHEMICAL SYNTHESIS, 3-D STRUCTURE IN SOLUTION, PHARMACOLOGY AND DOCKING ON K+ CHANNELS
 
Authors :  A. Mosbah, B. Jouirou, V. Visan, S. Grissmer, M. El Ayeb, H. Rochat, M. De Waard, K. Mabrouk, J. M. Sabatier
Date :  03 Jun 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cobatoxin 1, Scorpion Toxin, Centuroides Noxius, K+ Channel, Chemical Synthesis, 3-D Structure, 1H-Nmr Spectroscopy, Circular Dichroism, Molecular Modeling, Docking Experiment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Jouirou, A. Mosbah, V. Visan, S. Grissmer, S. M'Barek, Z. Fajloun, J. Van Rietschoten, C. Devaux, H. Rochat, G. Lippens, M. El Ayeb, M. De Waard, K. Mabrouk, J. M. Sabatier
Cobatoxin 1 From Centruroides Noxius Scorpion Venom: Chemical Synthesis, Three-Dimensional Structure In Solution, Pharmacology And Docking On K+ Channels.
Biochem. J. V. 377 37 2004
PubMed-ID: 14498829  |  Reference-DOI: 10.1042/BJ20030977
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COBATOXIN 1
    Chains: A
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN CENTRUROIDES NOXIUS (MEXICAN SCORPION)
    Synonym: COTX1, GTIX
    Synthetic: YES

 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 1PJV)

(-) Sites  (0, 0)

(no "Site" information available for 1PJV)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:3 -A:22
2A:8 -A:27
3A:12 -A:29

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SCORP_SHORT_TOXINPS01138 Scorpion short toxins signature.KA101_CENNO36-57  1A:8-29

(-) Exons   (0, 0)

(no "Exon" information available for 1PJV)

(-) 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:32
 aligned with KA101_CENNO | O46028 from UniProtKB/Swiss-Prot  Length:62

    Alignment length:32
                                    38        48        58  
           KA101_CENNO   29 AVCVYRTCDKDCKRRGYRSGKCINNACKCYPY 60
               SCOP domains d1pjva_ A: Cobatoxin 1           SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains Toxin_2-1pjvA01 A:1-30        -- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------SCORP_SHORT_TOXIN     --- PROSITE
                 Transcript -------------------------------- Transcript
                  1pjv A  1 AVCVYRTCDKDCKRRGYRSGKCINNACKCYPY 32
                                    10        20        30
   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: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Knottin_1 (78)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (KA101_CENNO | O46028)
molecular function
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another 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 1pjv)
 
  Sites
(no "Sites" information available for 1pjv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pjv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  1pjv
    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
  KA101_CENNO | O46028
    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
  KA101_CENNO | O46028
    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 1PJV)

(-) Related Entries Specified in the PDB File

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