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(-) Description

Title :  SOLUTION STRUCTURE OF THE HUMAN BMX SH2 DOMAIN
 
Authors :  T. Kasai, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh2 Domain, Phosphotyrosine Binding Domain, Protein Tyrosine Kinase, Signal Transduction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kasai, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Human Bmx Sh2 Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOPLASMIC TYROSINE-PROTEIN KINASE BMX
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression System PlasmidP061225-65
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GeneBMX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymBONE MARROW TYROSINE KINASE GENE IN CHROMOSOME X PROTEIN, EPITHELIAL AND ENDOTHELIAL TYROSINE KINASE, ETK, NTK38

 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 2EKX)

(-) Sites  (0, 0)

(no "Site" information available for 2EKX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.BMX_HUMAN296-392  1A:13-109

(-) Exons   (7, 7)

NMR Structure (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003576071ENSE00001415013X:15482369-15482547179BMX_HUMAN-00--
1.4bENST000003576074bENSE00000857421X:15526468-15526614147BMX_HUMAN1-46460--
1.5ENST000003576075ENSE00000665881X:15527452-15527556105BMX_HUMAN47-81350--
1.6ENST000003576076ENSE00000665880X:15529560-1552964182BMX_HUMAN82-109280--
1.7ENST000003576077ENSE00000665879X:15534235-15534354120BMX_HUMAN109-149410--
1.8bENST000003576078bENSE00000665878X:15536052-1553611665BMX_HUMAN149-170220--
1.9ENST000003576079ENSE00000665876X:15540469-15540710242BMX_HUMAN171-251811A:1-22
1.10ENST0000035760710ENSE00000665875X:15543411-1554348878BMX_HUMAN251-277271A:2-65
1.11ENST0000035760711ENSE00000665874X:15544165-1554421854BMX_HUMAN277-295191A:7-126
1.12ENST0000035760712ENSE00000665873X:15548096-1554815055BMX_HUMAN295-313191A:12-3019
1.13ENST0000035760713ENSE00000665872X:15549451-1554953080BMX_HUMAN314-340271A:31-5727
1.14ENST0000035760714ENSE00000665871X:15552335-15552462128BMX_HUMAN340-383441A:57-10044
1.15ENST0000035760715ENSE00000665870X:15554476-1555455075BMX_HUMAN383-408261A:100-11011
1.16ENST0000035760716ENSE00000665869X:15555257-15555428172BMX_HUMAN408-465580--
1.17aENST0000035760717aENSE00000665868X:15560105-15560321217BMX_HUMAN465-537730--
1.18bENST0000035760718bENSE00000665867X:15561194-1556125865BMX_HUMAN538-559220--
1.19ENST0000035760719ENSE00000665865X:15564926-15565044119BMX_HUMAN559-599410--
1.20ENST0000035760720ENSE00001434621X:15567963-15568120158BMX_HUMAN599-651530--
1.21bENST0000035760721bENSE00001484764X:15574196-15574652457BMX_HUMAN652-675240--

(-) 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:110
 aligned with BMX_HUMAN | P51813 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:144
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389    
            BMX_HUMAN   250 KSSSSSEDVASSNQKERNVNHTTSKISWEFPESSSSEEEENLDDYDWFAGNISRSQSEQLLRQKGKEGAFMVRNSSQVGMYTVSLFSKAVNDKKGTVKHYHVHTNAENKLYLAENYCFDSIPKLIHYHQHNSAGMITRLRHPVS 393
               SCOP domains d2ekxa                                  _ A: automated matches                                                                                   SCOP domains
               CATH domains ----------------------------------------------2ekxA01 A:13-109 SHC Adaptor Protein                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......----------------------------------............hhhhhhhhhhhh....eeeeee......eeeee............eeee.ee.....ee........hhhhhhhhhhhh.........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------SH2  PDB: A:13-109 UniProt: 296-392                                                              - PROSITE
           Transcript 1 (1) -Exon 1.10  PDB: A:2-6      -----------------Exon 1.12          Exon 1.13  PDB: A:31-57    ------------------------------------------Exon 1.15   Transcript 1 (1)
           Transcript 1 (2) 1.-------------------------Exon 1.11          --------------------------------------------Exon 1.14  PDB: A:57-100 UniProt: 340-383   ---------- Transcript 1 (2)
                 2ekx A   1 GSSGSS----------------------------------GLDDYDWFAGNISRSQSEQLLRQKGKEGAFMVRNSSQVGMYTVSLFSKAVNDKKGTVKHYHVHTNAENKLYLAENYCFDSIPKLIHYHQHNSAGMITRLRHPVS 110
                                 |   -         -         -         -|       16        26        36        46        56        66        76        86        96       106    
                                 6                                  7                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (BMX_HUMAN | P51813)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    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: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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    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.
biological process
    GO:0001865    NK T cell differentiation    The process in which a precursor cell type acquires the specialized features of a NK T cell.
    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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0006921    cellular component disassembly involved in execution phase of apoptosis    The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0007498    mesoderm development    The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    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: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:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BMX_HUMAN | P518132ys2 3sxr 3sxs

(-) Related Entries Specified in the PDB File

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