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 :  SOLUTION STRUCTURE OF SCYTOVIRIN REFINED AGAINST RESIDUAL DIPOLAR COUPLINGS
 
Authors :  R. L. Mcfeeters, R. A. Byrd
Date :  07 Dec 06  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Sugar Binding Protein, Antiviral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Mcfeeters, C. Xiong, B. R. O'Keefe, H. R. Bokesch, J. B. Mcmahon, D. M. Ratner, R. Castelli, P. H. Seeberger, R. A. Byrd
The Novel Fold Of Scytovirin Reveals A New Twist For Antiviral Entry Inhibitors
J. Mol. Biol. V. 369 451 2007
PubMed-ID: 17434526  |  Reference-DOI: 10.1016/J.JMB.2007.03.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCYTOVIRIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET32
    Expression System Vector Type: VECTOR
    Organism Scientific: SCYTONEMA VARIUM
    Organism Taxid: 423208

 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 2JMV)

(-) Sites  (0, 0)

(no "Site" information available for 2JMV)

(-) SS Bonds  (6, 6)

NMR Structure
No.Residues
1A:7 -A:55
2A:20 -A:26
3A:32 -A:38
4A:68 -A:74
5A:74 -A:80
6A:80 -A:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JMV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JMV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JMV)

(-) 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:94
 aligned with SVN_SCYVA | P86041 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
             SVN_SCYVA    1 GSGPTYCWNEANNPGGPNRCSNNKQCDGARTCSSSGFCQGTSRKPDPGPKGPTYCWDEAKNPGGPNRCSNSKQCDGARTCSSSGFCQGTAGHAA 94
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  2jmv A  1 GSGPTYCWNEANNPGGPNRCSNNKQCDGARTCSSSGFCQGTSRKPDPGPKGPTYCWDEAKNPGGPNRCSNSKQCDGARTCSSSGFCQGTAGHAA 94
                                    10        20        30        40        50        60        70        80        90
   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  (0, 0)

(no "SCOP Domain" information available for 2JMV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JMV)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (SVN_SCYVA | P86041)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

 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 2jmv)
 
  Sites
(no "Sites" information available for 2jmv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jmv)
 

(-) 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
  2jmv
    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
  SVN_SCYVA | P86041
    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
  SVN_SCYVA | P86041
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SVN_SCYVA | P86041: 2qsk 2qt4

(-) Related Entries Specified in the PDB File

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