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(-) Description

Title :  SOLUTION STRUCTURE OF THE COMPLEX OF THE PTB DOMAIN OF SNT-2 AND 19-RESIDUE PEPTIDE (AA 1571-1589) OF HALK
 
Authors :  H. Li, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Date :  24 Feb 10  (Deposition) - 26 May 10  (Release) - 12 Feb 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Complex, Snt-2, Ptb Domain, Halk, Structural Genomics, Signaling Protein, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein-Oncoprotein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Koshiba, H. Li, Y. Motoda, T. Tomizawa, T. Kasai, N. Tochio, T. Yabuki, T. Harada, S. Watanabe, A. Tanaka, M. Shirouzu, T. Kigawa, T. Yamamoto, S. Yokoyama
Structural Basis For The Recognition Of Nucleophosmin-Anaplastic Lymphoma Kinase Oncoprotein By The Phosphotyrosine Binding Domain Of Suc1-Associated Neurotrophic Factor-Induced Tyrosine-Phosphorylated Target-
J. Struct. Funct. Genom. V. 11 125 2010
PubMed-ID: 20454865  |  Reference-DOI: 10.1007/S10969-010-9091-X

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR SUBSTRATE 3
    ChainsA
    EngineeredYES
    Expression SystemCELL-FREE SYNTHESIS
    Expression System VectorP060320-18
    Expression System Vector TypeVECTOR
    FragmentPTB DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFGFR SUBSTRATE 3, SUC1-ASSOCIATED NEUROTROPHIC FACTOR TARGET 2, SNT-2, FGFR-SIGNALING ADAPTOR SNT2
 
Molecule 2 - 19-RESIDUE PEPTIDE FROM ALK TYROSINE KINASE RECEPTOR
    ChainsB
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SynonymHALK, ANAPLASTIC LYMPHOMA KINASE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KUP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRS_PTBPS51064 IRS-type PTB domain profile.FRS3_HUMAN13-115  1A:13-115
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRS_PTBPS51064 IRS-type PTB domain profile.FRS3_HUMAN13-115  1A:13-115

(-) Exons   (0, 0)

(no "Exon" information available for 2KUP)

(-) 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:146
 aligned with FRS3_HUMAN | O43559 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
          FRS3_HUMAN      1 MGSCCSCLNRDSVPDNHPTKFKVTNVDDEGVELGSGVMELTQSELVLHLHRREAVRWPYLCLRRYGYDSNLFSFESGRRCQTGQGIFAFKCSRAEEIFNLLQDLMQCNSINVMEEPVIITRNSHPAELDLPRAPQPPNALGYTVSS  146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------IRS-2kupA01 A:16-109                                                                          ------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeee.......eeeeee.....eeee......eee......eee.....eeeee........eeeeee...hhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------IRS_PTB  PDB: A:13-115 UniProt: 13-115                                                                 ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2kup A    1 GSSGSSGLNRDSVPDNHPTKFKVTNVDDEGVELGSGVMELTQSELVLHLHRREAVRWPYLCLRRYGYDSNLFSFESGRRCQTGQGIFAFKCSRAEEIFNLLQDLMQCNSINVMEEPVIITRNSHPAELDLPRAPQPPNALGYTVSS  146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with ALK_HUMAN | Q9UM73 from UniProtKB/Swiss-Prot  Length:1620

    Alignment length:19
                                  1580         
           ALK_HUMAN   1571 LFRLRHFPCGNVNYGYQQQ 1589
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ...........eee..... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                2kup B    1 LFRLRHFPCGNVNYGYQQQ   19
                                    10         

   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 2KUP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (36, 42)

NMR Structure(hide GO term definitions)
Chain A   (FRS3_HUMAN | O43559)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. 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:0005104    fibroblast growth factor receptor binding    Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving 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.
    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.

Chain B   (ALK_HUMAN | Q9UM73)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004704    NF-kappaB-inducing kinase activity    Catalysis of the phosphorylation of the alpha or beta subunit of the inhibitor of kappaB kinase complex (IKK).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase 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: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007169    transmembrane receptor protein tyrosine kinase 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 tyrosine kinase 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: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.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALK_HUMAN | Q9UM732kuq 2xb7 2xba 2xp2 2yfx 2yhv 2yjr 2yjs 2ys5 2yt2 3aox 3l9p 3lcs 3lct 4anl 4anq 4ans 4ccb 4ccu 4cd0 4cli 4clj 4cmo 4cmt 4cmu 4cnh 4ctb 4ctc 4dce 4fnw 4fnx 4fny 4fnz 4fob 4foc 4fod 4joa 4mkc 4tt7 4z55 5a9u 5aa8 5aa9 5aaa 5aab 5aac 5fto 5ftq 5imx 5iug 5iuh 5iui 5j7h 5kz0
        FRS3_HUMAN | O435592kuq 2ys5 2yt2

(-) Related Entries Specified in the PDB File

2ys5 AMBER MINIMIZATION