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 :  SOLUTION STRUCTURE OF THE C-TERMINAL PLECKSTRIN HOMOLOGY DOMAIN OF SBF1 FROM MOUSE
 
Authors :  H. Li, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Nov 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sbf1, Mtmr5, The Pleckstrin Homology Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The C-Terminal Pleckstrin Homology Domain Of Sbf1 From Mouse
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SET BINDING FACTOR 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP030212-74
    Expression System Vector TypePLASMID
    FragmentTHE PLECKSTRIN HOMOLOGY DOMAIN
    GeneRIKEN CDNA 2610510A08
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymSBF1

 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 1V5U)

(-) Sites  (0, 0)

(no "Site" information available for 1V5U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5U)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.MTMR5_MOUSE1761-1865  1A:9-111

(-) Exons   (0, 0)

(no "Exon" information available for 1V5U)

(-) 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:117
 aligned with MTMR5_MOUSE | Q6ZPE2 from UniProtKB/Swiss-Prot  Length:1867

    Alignment length:139
                                                                                                                                                               1867    
                                  1742      1752      1762      1772      1782      1792      1802      1812      1822      1832      1842      1852      1862    |    
         MTMR5_MOUSE   1733 GSTTSSSRQAARRSTSTLYSQFQTAESENRSYEGILYKKGAFMKPWKARWFVLDKTKHQLRYYDHRMDTECKGVIDLAEVEAVAPGTPTIGAPKTVDEKAFFDVKTTRRVYNFCAQDVPSAQQWVDRIQSCLSDA----    -
               SCOP domains d1v5ua_                       A: SET binding factor 1, Sbf1                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------PH-1v5uA01 A:9-111                                                                                     ------ Pfam domains
         Sec.struct. author ........----------------------.eeeeeee........eeeeeeee....eeeee..........eee...eeeee.................eeeee..eeeeee...hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------PH_DOMAIN  PDB: A:9-111 UniProt: 1761-1865                                                               ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1v5u A    1 GSSGSSGR----------------------SYEGILYKKGAFMKPWKARWFVLDKTKHQLRYYDHRMDTECKGVIDLAEVEAVAPGTPTIGAPKTVDEKAFFDVKTTRRVYNFCAQDVPSAQQWVDRIQSCLSSGPSSG  117
                                   | -         -         -|       18        28        38        48        58        68        78        88        98       108         
                                   8                      9                                                                                                            

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V5U)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PH (111)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (MTMR5_MOUSE | Q6ZPE2)
molecular function
    GO:0017112    Rab guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rab family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019208    phosphatase regulator activity    Modulates the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule.
    GO:0001691    pseudophosphatase activity    Maintains the phosphorylation state of certain molecules by associating with them and preventing them from associating with active phosphatases, and thus inhibiting the enzyme activity without interacting with the enzyme. Often pertains to proteins belonging to dual-specificity phosphatase family but lacking critical active site residues.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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 1v5u)
 
  Sites
(no "Sites" information available for 1v5u)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v5u)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1v5u
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MTMR5_MOUSE | Q6ZPE2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MTMR5_MOUSE | Q6ZPE2
    Protein Disorder PredictionDisEMBL | 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 1V5U)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V5U)