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 - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF CONTRYPHAN-VN
 
Authors :  T. Eliseo, D. O. Cicero, F. Polticelli, M. E. Schinina, G. R. Massilia, M. Paci, P. Ascenzi
Date :  11 Feb 03  (Deposition) - 04 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  D-Tryptophan, Cyclic Peptide, Disulfide Bridge, Cis-Trans Isomerism, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Eliseo, D. O. Cicero, C. Romeo, M. E. Schinina, G. R. Massilia, F. Polticelli, P. Ascenzi, M. Paci
Solution Structure Of The Cyclic Peptide Contryphan-Vn, A Ca2+-Dependent K+ Channel Modulator
Biopolymers V. 74 189 2004
PubMed-ID: 15150794  |  Reference-DOI: 10.1002/BIP.20025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONTRYPHAN-VN, MAJOR FORM (CIS CONFORMER)
    Chains: A
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN THE VENOM DUCT OF CONUS VENTRICOSUS (MARINE CONE SNAIL).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

NMR Structure (2, 2)
No.NameCountTypeFull Name
1DTR1Mod. Amino AcidD-TRYPTOPHAN
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:8 , CYS A:9BINDING SITE FOR RESIDUE NH2 A 10

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:3 -A:9

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Cys A:3 -Pro A:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONTRYPHANPS60027 Contryphan family signature.COW_CONVE3-9  1A:3-9

(-) Exons   (0, 0)

(no "Exon" information available for 1NXN)

(-) 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:10
 aligned with COW_CONVE | P83047 from UniProtKB/Swiss-Prot  Length:9

    Alignment length:10
                                    9 
                                    |-
             COW_CONVE    1 GDCPWKPWC-  -
               SCOP domains d1nxna_ A: SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE --CONTRYP- PROSITE
                 Transcript ---------- Transcript
                  1nxn A  1 GDCPxKPWCx 10
                                |   10
                                |    |
                                5-DTR|
                                    10-NH2
   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 1NXN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NXN)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (COW_CONVE | P83047)
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
    DTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:3 - Pro A:4   [ RasMol ]  
 

(-) 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 - model 1, sites 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
  1nxn
    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
  COW_CONVE | P83047
    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
  COW_CONVE | P83047
    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 1NXN)

(-) Related Entries Specified in the PDB File

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