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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OF HUMAN PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM 4 VARIANT
 
Authors :  M. Yoneyama, K. Saito, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 May 05  (Deposition) - 17 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Fibronectin Type Iii Domain Containing Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yoneyama, K. Saito, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Fibronectin Type-Iii Domain Of Human Protein Tyrosine Phosphatase, Receptor Type, D Isoform 4 Variant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression System PlasmidP050131-05
    Expression System Vector TypePLASMID
    FragmentFIBRONECTIN TYPE-III DOMAIN
    GenePTPRD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPROTEIN-TYROSINE PHOSPHATASE DELTA, R-PTP-DELTA, PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, D ISOFORM 4

 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 1X5Z)

(-) Sites  (0, 0)

(no "Site" information available for 1X5Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X5Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X5Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X5Z)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.PTPRD_HUMAN325-415
420-516
518-607
612-709
714-822
921-1016
823-916
1020-1106
  2-
-
A:20-109
A:112-114
-
-
-
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003811961ENSE00001811856chr9:9938610-9938507104PTPRD_HUMAN-00--
1.2ENST000003811962ENSE00001948254chr9:9766851-976681042PTPRD_HUMAN-00--
1.3ENST000003811963ENSE00001955782chr9:9734571-973453339PTPRD_HUMAN-00--
1.4ENST000003811964ENSE00001889688chr9:9574781-957473250PTPRD_HUMAN-00--
1.6ENST000003811966ENSE00001817715chr9:9397482-939744934PTPRD_HUMAN-00--
1.7ENST000003811967ENSE00001940698chr9:9183363-918330460PTPRD_HUMAN-00--
1.8ENST000003811968ENSE00001487965chr9:9018735-901869739PTPRD_HUMAN-00--
1.10bENST0000038119610bENSE00001254389chr9:8733946-8733780167PTPRD_HUMAN1-22220--
1.11ENST0000038119611ENSE00001172744chr9:8636844-8636699146PTPRD_HUMAN22-70490--
1.12cENST0000038119612cENSE00001172741chr9:8633458-8633317142PTPRD_HUMAN71-118480--
1.13ENST0000038119613ENSE00001172738chr9:8528779-8528591189PTPRD_HUMAN118-181640--
1.15ENST0000038119615ENSE00001780939chr9:8527353-85273459PTPRD_HUMAN181-18440--
1.16ENST0000038119616ENSE00001739974chr9:8526644-852662718PTPRD_HUMAN184-19070--
1.17bENST0000038119617bENSE00001087346chr9:8525035-8524925111PTPRD_HUMAN190-227380--
1.18ENST0000038119618ENSE00001662513chr9:8523524-852351312PTPRD_HUMAN227-23150--
1.19bENST0000038119619bENSE00001087338chr9:8521546-8521277270PTPRD_HUMAN231-321910--
1.20ENST0000038119620ENSE00001012020chr9:8518429-8517848582PTPRD_HUMAN321-5151951A:1-1717
1.21ENST0000038119621ENSE00001172713chr9:8507434-8507301134PTPRD_HUMAN515-559451A:17-6145
1.22aENST0000038119622aENSE00001368106chr9:8504405-8504261145PTPRD_HUMAN560-608491A:62-10948
1.23ENST0000038119623ENSE00001012029chr9:8501059-8500754306PTPRD_HUMAN608-7101031A:110-1156
1.24ENST0000038119624ENSE00001012019chr9:8499840-8499647194PTPRD_HUMAN710-774650--
1.25ENST0000038119625ENSE00001172700chr9:8497268-849724227PTPRD_HUMAN775-78390--
1.26ENST0000038119626ENSE00001012012chr9:8492979-8492862118PTPRD_HUMAN784-823400--
1.27bENST0000038119627bENSE00001012016chr9:8486349-8485762588PTPRD_HUMAN823-10191970--
1.28bENST0000038119628bENSE00001012033chr9:8485324-848522798PTPRD_HUMAN1019-1051330--
1.29bENST0000038119629bENSE00001012014chr9:8484378-8484119260PTPRD_HUMAN1052-1138870--
1.30ENST0000038119630ENSE00001172680chr9:8471085-847099591PTPRD_HUMAN1138-1168310--
1.31ENST0000038119631ENSE00001012036chr9:8465675-8465466210PTPRD_HUMAN1169-1238700--
1.32ENST0000038119632ENSE00001012037chr9:8460571-8460411161PTPRD_HUMAN1239-1292540--
1.34ENST0000038119634ENSE00001172661chr9:8449837-8449725113PTPRD_HUMAN1292-1330390--
1.36ENST0000038119636ENSE00001172655chr9:8436689-843659298PTPRD_HUMAN1330-1362330--
1.37ENST0000038119637ENSE00001012032chr9:8404660-8404537124PTPRD_HUMAN1363-1404420--
1.38ENST0000038119638ENSE00001172638chr9:8389407-8389232176PTPRD_HUMAN1404-1462590--
1.39ENST0000038119639ENSE00001012031chr9:8376726-8376607120PTPRD_HUMAN1463-1502400--
1.40ENST0000038119640ENSE00001012034chr9:8376090-8375936155PTPRD_HUMAN1503-1554520--
1.41ENST0000038119641ENSE00001172619chr9:8341978-8341693286PTPRD_HUMAN1554-1649960--
1.42ENST0000038119642ENSE00001172611chr9:8341268-8341090179PTPRD_HUMAN1650-1709600--
1.43ENST0000038119643ENSE00001012021chr9:8340469-8340343127PTPRD_HUMAN1709-1751430--
1.44ENST0000038119644ENSE00001656481chr9:8339047-8338922126PTPRD_HUMAN1752-1793420--
1.45ENST0000038119645ENSE00001707976chr9:8331736-8331582155PTPRD_HUMAN1794-1845520--
1.46ENST0000038119646ENSE00001012025chr9:8319966-8319831136PTPRD_HUMAN1845-1890460--
1.47cENST0000038119647cENSE00001254378chr9:8317942-83142463697PTPRD_HUMAN1891-1912220--
1.49aENST0000038119649aENSE00001922875chr9:10612509-10612398112PTPRD_HUMAN-00--
1.50aENST0000038119650aENSE00001820932chr9:10341062-10340963100PTPRD_HUMAN-00--
1.51ENST0000038119651ENSE00001895238chr9:10033790-1003371873PTPRD_HUMAN-00--

(-) 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:115
 aligned with PTPRD_HUMAN | P23468 from UniProtKB/Swiss-Prot  Length:1912

    Alignment length:126
                                   508       518       528       538       548       558       568       578       588       598       608       618      
          PTPRD_HUMAN   499 GDGPLSSDIQVITQTGVPGQPLNFKAEPESETSILLSWTPPRSDTIANYELVYKDGEHGEEQRITIEPGTSYRLQGLKPNSLYYFRLAARSPQGLGASTAEISARTMQSKPSAPPQDISCTSPSST 624
               SCOP domains -------d1x5za1 A:8-109 Receptor-type tyrosine-protein phosphatase delta, PTPRD                               ----------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------fn3-1x5zA01 A:19-99                                                              --------------------------- Pfam domains
         Sec.struct. author .....................eeeeee.....eeeeeee........eeee..ee.........ee....eeeee......eeee.eeee....eeee...eeee....-----------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE FN3  PDB: -       -FN3  PDB: A:20-109 UniProt: 518-607                                                       ----FN3           PROSITE
           Transcript 1 (1) Exon 1.20        --------------------------------------------Exon 1.22a  PDB: A:62-109 UniProt: 560-608       ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.21  PDB: A:17-61 UniProt: 515-559     ------------------------------------------------Exon 1.23         Transcript 1 (2)
                 1x5z A   1 GSSGSSGDIQVITQTGVPGQPLNFKAEPESETSILLSWTPPRSDTIANYELVYKDGEHGEEQRITIEPGTSYRLQGLKPNSLYYFRLAARSPQGLGASTAEISARTMQS-----------SGPSSG 115
                                    10        20        30        40        50        60        70        80        90       100        |-         -|     
                                                                                                                                      109         110     

   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 1X5Z)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: E-set (290)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (PTPRD_HUMAN | P23468)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
    GO:0050775    positive regulation of dendrite morphogenesis    Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis.
    GO:0097105    presynaptic membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a presynaptic membrane, including any proteins associated with the membrane, but excluding other cellular components. A presynaptic membrane is a specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0007185    transmembrane receptor protein tyrosine phosphatase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTPRD_HUMAN | P234682dlh 2yd6 2yd7 4rca

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