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 THE GYF DOMAIN OF A HYPOTHETICAL PROTEIN FROM ARABIDOPSIS THALIANA
 
Authors :  N. Nameki, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Gyf Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nameki, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Gyf Domain Of A Hypothetical Protein From Arabidopsis Thaliana
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AT5G08430
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030107-37
    Expression System Vector Type: PLASMID
    Fragment: GYF DOMAIN
    Gene: RIKEN CDNA RAFL09-47-K03
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: 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 1WH2)

(-) Sites  (0, 0)

(no "Site" information available for 1WH2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WH2)

(-) 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, 20Gly A:31 -Pro A:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WH2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GYFPS50829 GYF domain profile.Y5843_ARATH497-551  1A:17-71

(-) Exons   (0, 0)

(no "Exon" information available for 1WH2)

(-) 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:78
 aligned with Y5843_ARATH | Q9FT92 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:105
                                                                                                                             553     
                                   463       473       483       493       503       513       523       533       543       553     
          Y5843_ARATH   454 GSQVQPNPSEVIELSDDDEDDNGDGETLDPKVEDVRVLSYDKEKLNWLYKDPQGLVQGPFSLTQLKAWSDAEYFTKQFRVWMTGESMESAVLLTDVLRLV-----   -
               SCOP domains d1   wh2a                        _ A: Hypothetical rotein At5g08430                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------GYF-1wh2A01 A:18-70                                  -------- Pfam domains
         Sec.struct. author ..---....------------------------.............eeee.....eeeeehhhhhhhhhh........eeee........eehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------GYF  PDB: A:17-71 UniProt: 497-551                     ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1wh2 A   1 GS---SGSS------------------------GVRVLSYDKEKLNWLYKDPQGLVQGPFSLTQLKAWSDAEYFTKQFRVWMTGESMESAVLLTDVLRLSGPSSG  78
                             |   |  |-         -         -   |    13        23        33        43        53        63        73     
                             2   3  6                        7
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WH2)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: GYF] (4)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (Y5843_ARATH | Q9FT92)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

 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 1wh2)
 
  Sites
(no "Sites" information available for 1wh2)
 
  Cis Peptide Bonds
    Gly A:31 - Pro A:32   [ 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 - 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
  1wh2
    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
  Y5843_ARATH | Q9FT92
    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
  Y5843_ARATH | Q9FT92
    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
        Y5843_ARATH | Q9FT92: 1v32

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WH2)