Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
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 THE HYPOTHETICAL ENTH-VHS DOMAIN AT3G16270 FROM ARABIDOPSIS THALIANA
 
Authors :  B. Lopez-Mendez, D. Pantoja-Uceda, T. Tomizawa, S. Koshiba, T. Kigawa, M. Shirouzu, T. Terada, M. Inoue, T. Yabuki, M. Aoki, E. Seki T. Matsuda, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, M. Seki, K. Shinozaki, S. Yokoyama, P. Guntert, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Mar 04  (Deposition) - 03 May 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hypothetical Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Lopez-Mendez, D. Pantoja-Uceda, T. Tomizawa, S. Koshiba, T. Kigawa, M. Shirouzu, T. Terada, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, M. Seki, K. Shinozaki, S. Yokoyama, P. Guntert
Solution Structure Of The Hypothetical Enth-Vhs Domain At3G16270 From Arabidopsis Thaliana
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN (RAFL09-17-B18)
    Chains: A
    Engineered: YES
    Expression System Plasmid: P021216-68
    Expression System Vector Type: PLASMID
    Fragment: ENTH-VHS HYPOTHETICAL DOMAIN
    Gene: RIKEN CDNA RAFL09-17-B18
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: E.COLI CELL-FREE PROTEIN SYNTHESIS

 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 1VDY)

(-) Sites  (0, 0)

(no "Site" information available for 1VDY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.Y3627_ARATH35-89  1A:34-88

(-) Exons   (0, 0)

(no "Exon" information available for 1VDY)

(-) 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:140
 aligned with Y3627_ARATH | Q9C5H4 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          Y3627_ARATH     2 DTSRRAVESYWRSRMIDAVTSDEDKVAPVYKLEEICDLLRSSHVSIVKEFSEFILKRLDNKSPIVKQKALRLIKYAVGKSGSEFRREMQRNSVAVRNLFHYKGHPDPLKGDALNKAVRETAHETISAIFSEENGTKPAAPESINRRIEG 150
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------ENTH-1vdyA01 A:13-133                                                                                                    ---------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh..........---------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------VHS  PDB: A:34-88 UniProt: 35-89                       ------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdy A   1 GSSGSSGESYWRSRMIDAVTSDEDKVAPVYKLEEICDLLRSSHVSIVKEFSEFILKRLDNKSPIVKQKALRLIKYAVGKSGSEFRREMQRNSVAVRNLFHYKGHPDPLKGDALNKAVRETAHETISAIFSEENGSGPSS---------G 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-        |
                                                                                                                                                                    139       140
   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 1VDY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: ENTH_VHS (15)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (Y3627_ARATH | Q9C5H4)
biological process
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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

(-) 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
  1vdy
    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
  Y3627_ARATH | Q9C5H4
    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
  Y3627_ARATH | Q9C5H4
    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
        Y3627_ARATH | Q9C5H4: 2dcp

(-) Related Entries Specified in the PDB File

5928 CHEMICAL SHIFT DATA RELATED ID: ATR001000337 RELATED DB: TARGETDB