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 STRUCTURE OF VONTR
 
Authors :  J. L. Dutton, R. F. Renda, C. Waine, R. J. Clark, N. L. Daly, C. V. Jennings, M. A. Anderson, D. J. Craik
Date :  27 Jul 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Helix, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Dutton, R. F. Renda, C. Waine, R. J. Clark, N. L. Daly, C. V. Jennings, M. A. Anderson, D. J. Craik
Conserved Structural And Sequence Elements Implicated In The Processing Of Gene-Encoded Circular Proteins
J. Biol. Chem. V. 279 46858 2004
PubMed-ID: 15328347  |  Reference-DOI: 10.1074/JBC.M407421200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VONTR PROTEIN
    Chains: A
    Engineered: YES
    Fragment: N-TERMINAL REPEAT FRAGMENT
    Other Details: THIS IS A SYNTHETIC PEPTIDE BASED ON THE CYCLOTIDE PRECURSOR PROTEIN FROM VIOLA ODORATA
    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 1WN4)

(-) Sites  (0, 0)

(no "Site" information available for 1WN4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WN4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYCLOTIDEPS51052 Cyclotides profile.VARA_VIOOD67-95
121-149
175-203		  1-
-
A:26-28

(-) Exons   (0, 0)

(no "Exon" information available for 1WN4)

(-) 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:28
 aligned with VARA_VIOOD | Q5USN7 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:28
                                   159       169        
           VARA_VIOOD   150 ALETQKPNHLLEEALVAFAKKGNLGGLP 177
               SCOP domains d1wn4a_ A: Cyclotide k1      SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE -------------------------CYC PROSITE
                 Transcript ---------------------------- Transcript
                 1wn4 A   1 ALETQKPNHLLEEALVAFAKKGNLGGLP  28
                                    10        20
   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 1WN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WN4)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (VARA_VIOOD | Q5USN7)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.

 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 1wn4)
 
  Sites
(no "Sites" information available for 1wn4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wn4)
 

(-) 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
  1wn4
    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
  VARA_VIOOD | Q5USN7
    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
  VARA_VIOOD | Q5USN7
    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 1WN4)

(-) Related Entries Specified in the PDB File

1wn8 SYN PEPTIDE BASED ON N-TERMINAL REPEAT SEQUENCE OF CYCLOTIDE PRECURSORS