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(-) Description

Title :  STRUCTURE, SULFATIDE-BINDING PROPERTIES, AND INHIBITION OF PLATELET AGGREGATION BY A DISABLED-2-DERIVED PEPTIDE
 
Authors :  S. Xiao
Date :  08 May 12  (Deposition) - 19 Sep 12  (Release) - 21 Nov 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Platelet Aggregation Inhibitor, Sulfatides, Dodecylphosphocholine, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Xiao, J. J. Charonko, X. Fu, A. Salmanzadeh, R. V. Davalos, P. P. Vlachos, C. V. Finkielstein, D. G. Capelluto
Structure, Sulfatide Binding Properties, And Inhibition Of Platelet Aggregation By A Disabled-2 Protein-Derived Peptide.
J. Biol. Chem. V. 287 37691 2012
PubMed-ID: 22977233  |  Reference-DOI: 10.1074/JBC.M112.385609

(-) Compounds

Molecule 1 - DISABLED HOMOLOG 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNIPROT RESIDUES 24-58
    GeneDAB2, DOC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOC-2, DIFFERENTIALLY-EXPRESSED PROTEIN 2

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LSW)

(-) Sites  (0, 0)

(no "Site" information available for 2LSW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LSW)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DAB2_HUMAN45-196  1A:45-58
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.DAB2_HUMAN45-196  1A:45-58

(-) Exons   (0, 0)

(no "Exon" information available for 2LSW)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:35
 aligned with DAB2_HUMAN | P98082 from UniProtKB/Swiss-Prot  Length:770

    Alignment length:35
                                    33        43        53     
            DAB2_HUMAN   24 SKKEKKKGPEKTDEYLLARFKGDGVKYKAKLIGID 58
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ---------------------PID            PROSITE
                 Transcript ----------------------------------- Transcript
                  2lsw A 24 SKKEKKKGPEKTDEYLLARFKGDGVKYKAKLIGID 58
                                    33        43        53     

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  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 2LSW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

NMR Structure(hide GO term definitions)
Chain A   (DAB2_HUMAN | P98082)
molecular function
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0038024    cargo receptor activity    Combining selectively with an extracellular substance and delivering the substance into the cell via endocytosis.
    GO:0035615    clathrin adaptor activity    The binding activity of a molecule that brings together clathrin and one or more other molecules, permitting them to function in a coordinated way.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035026    leading edge cell differentiation    The process in which relatively unspecialized cells acquire specialized structural and/or functional features of leading edge cells, cells at the front of a migrating epithelial sheet.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0060766    negative regulation of androgen receptor signaling pathway    Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:1903077    negative regulation of protein localization to plasma membrane    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0060391    positive regulation of SMAD protein import into nucleus    Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:2000096    positive regulation of Wnt signaling pathway, planar cell polarity pathway    Any process that activates or increases the frequency, rate or extent of Wnt signaling pathway, planar cell polarity pathway.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:2000370    positive regulation of clathrin-dependent endocytosis    Any process that activates or increases the frequency, rate or extent of clathrin-mediated endocytosis.
    GO:2000643    positive regulation of early endosome to late endosome transport    Any process that activates or increases the frequency, rate or extent of early endosome to late endosome transport.
    GO:0045807    positive regulation of endocytosis    Any process that activates or increases the frequency, rate or extent of endocytosis.
    GO:0010718    positive regulation of epithelial to mesenchymal transition    Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030511    positive regulation of transforming growth factor beta receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0030665    clathrin-coated vesicle membrane    The lipid bilayer surrounding a clathrin-coated vesicle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0070022    transforming growth factor beta receptor complex    A homodimeric receptor complex that consists of two TGF-beta receptor monomers.

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