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(-) Description

Title :  3D STRUCTURE PREDICTION OF THE IG2-IG4 DOMAINS OF THE ECTODOMAIN REGION OF THE HUMAN HEPATOCYTE GROWTH FACTOR-SCATTER FACTOR RECEPTOR, MET
 
Authors :  R. N. Miguel, T. L. Blundell, E. Gherardi
Date :  10 Feb 06  (Deposition) - 21 Feb 06  (Release) - 22 Mar 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Transferase, Glycoprotein, Hepatocyte Growth Factor-Scatter Factor Receptor, Met-Receptor, Proto-Oncogene, Tyrosine- Protein Kinase, Alternative Splicing, Atp-Binding, Chromosomal Translocation, Disease Mutation, Kinase, Membrane, Nucleotide-Binding, Phosphorylation, Receptor, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Gherardi, S. Sandin, M. V. Petoukhov, J. Finch, M. E. Youles, L. G. Ofverstedt, R. N. Miguel, T. L. Blundell, G. F. Vande Woude, U. Skoglund, D. I. Svergun
Structural Basis Of Hepatocyte Growth Factor/Scatter Factor And Met Signalling.
Proc. Natl. Acad. Sci. Usa V. 103 4046 2006
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR RECEPTOR
    ChainsA
    EC Number2.7.1.112
    EngineeredYES
    FragmentIG2-IG4 DOMAINS, RESIDUES 657-928
    SynonymHEPATOCYTE GROWTH FACTOR-SCATTER FACTOR RECEPTOR, MET PROTO-ONCOGENE TYROSINE KINASE, C-MET, HGF RECEPTOR, HGF-SF RECEPTOR
    SyntheticYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2CEW)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:697 -A:709
2A:790 -A:801
3A:882 -A:894

(-) Cis Peptide Bonds  (2, 2)

Theoretical Model
No.Residues
1Ser A:663 -Pro A:664
2His A:748 -Pro A:749

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032481P773LMET_HUMANUnclassified771333219AP773L
2UniProtVAR_075757F841VMET_HUMANDisease (DFNB97)794728016AF841V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CEW)

(-) Exons   (6, 6)

Theoretical Model (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003977521cENSE00001865305chr7:116312446-116312631186MET_HUMAN-00--
1.3cENST000003977523cENSE00001238915chr7:116339125-1163403381214MET_HUMAN1-4004000--
1.6ENST000003977526ENSE00000717722chr7:116371722-116371913192MET_HUMAN401-464640--
1.7ENST000003977527ENSE00000717724chr7:116380004-116380138135MET_HUMAN465-509450--
1.8ENST000003977528ENSE00000717726chr7:116380906-116381079174MET_HUMAN510-567580--
1.9bENST000003977529bENSE00000717728chr7:116395409-116395569161MET_HUMAN568-621540--
1.10ENST0000039775210ENSE00000717730chr7:116397491-116397593103MET_HUMAN621-655350--
1.11bENST0000039775211bENSE00000717732chr7:116397692-116397828137MET_HUMAN656-701461A:657-70145
1.12aENST0000039775212aENSE00000717735chr7:116398513-116398674162MET_HUMAN701-755551A:701-75555
1.13bENST0000039775213bENSE00001530016chr7:116399445-116399544100MET_HUMAN755-788341A:755-78834
1.14ENST0000039775214ENSE00000717791chr7:116403104-116403322219MET_HUMAN789-861731A:789-86173
1.15aENST0000039775215aENSE00000717803chr7:116409699-116409845147MET_HUMAN862-910491A:862-91049
1.16ENST0000039775216ENSE00000717811chr7:116411552-116411708157MET_HUMAN911-963531A:911-92818
1.17ENST0000039775217ENSE00000717833chr7:116411903-116412043141MET_HUMAN963-1010480--
1.18bENST0000039775218bENSE00000717861chr7:116414935-116415165231MET_HUMAN1010-1087780--
1.19ENST0000039775219ENSE00000717879chr7:116417443-11641752381MET_HUMAN1087-1114280--
1.20ENST0000039775220ENSE00000717895chr7:116418830-116419011182MET_HUMAN1114-1174610--
1.21ENST0000039775221ENSE00000717902chr7:116422042-116422151110MET_HUMAN1175-1211370--
1.22ENST0000039775222ENSE00000717928chr7:116423358-116423523166MET_HUMAN1211-1266560--
1.23ENST0000039775223ENSE00000717937chr7:116435709-116435845137MET_HUMAN1267-1312460--
1.24bENST0000039775224bENSE00000881894chr7:116435941-1164384402500MET_HUMAN1312-1390790--

(-) Sequences/Alignments

Theoretical Model
   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:272
 aligned with MET_HUMAN | P08581 from UniProtKB/Swiss-Prot  Length:1390

    Alignment length:272
                                   666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926  
            MET_HUMAN   657 PVITSISPKYGPMAGGTLLTLTGNYLNSGNSRHISIGGKTCTLKSVSNSILECYTPAQTISTEFAVKLKIDLANRETSIFSYREDPIVYEIHPTKSFISGGSTITGVGKNLNSVSVPRMVINVHEAGRNFTVACQHRSNSEIICCTTPSLQQLNLQLPLKTKAFFMLDGILSKYFDLIYVHNPVFKPFEKPVMISMGNENVLEIKGNDIDPEAVKGEVLKVGNKSCENIHLHSEAVLCTVPNDLLKLNSELNIEWKQAISSTVLGKVIVQPD 928
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee......eeeeeee........eeee..ee.eeeee...eeeee........eeeeeee.......eeeeee....eeeeee..ee......eeeeeee........eeeeeee....eeeee.eeee...eeeee......eeeee.ee.............eeeeee....eeeeee............eeeeee..........eeee..ee..eeee...eeee.........eeeeeee.........eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------L-------------------------------------------------------------------V--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: A:657-701 UniProt: 656-701  -----------------------------------------------------Exon 1.13b  PDB: A:755-788        Exon 1.14  PDB: A:789-861 UniProt: 789-861                               Exon 1.15a  PDB: A:862-910 UniProt: 862-910      Exon 1.16          Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.12a  PDB: A:701-755 UniProt: 701-755            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2cew A 657 PVITSISPKYGPMAGGTLLTLTGNYLNSGNSRHISIGGKTCTLKSVSNSILECYTPAQTISTEFAVKLKIDLANRETSIFSYREDPIVYEIHPTKSFISGGSTITGVGKNLNSVSVPRMVINVHEAGRNFTVACQHRSNSEIICCTTPSLQQLNLQLPLKTKAFFMLDGILSKYFDLIYVHNPVFKPFEKPVMISMGNENVLEIKGNDIDPEAVKGEVLKVGNKSCENIHLHSEAVLCTVPNDLLKLNSELNIEWKQAISSTVLGKVIVQPD 928
                                   666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926  

   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 2CEW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Theoretical Model(hide GO term definitions)
Chain A   (MET_HUMAN | P08581)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005008    hepatocyte growth factor-activated receptor activity    Combining with hepatocyte growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    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:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0001886    endothelial cell morphogenesis    The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
    GO:0048012    hepatocyte growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
    GO:0010507    negative regulation of autophagy    Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:1901299    negative regulation of hydrogen peroxide-mediated programmed cell death    Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.
    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:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:2001028    positive regulation of endothelial cell chemotaxis    Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    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:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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
        MET_HUMAN | P085811fyr 1r0p 1r1w 1shy 1ssl 1ux3 2g15 2rfn 2rfs 2uzx 2uzy 2wd1 2wgj 2wkm 3a4p 3bux 3c1x 3ccn 3cd8 3ce3 3cth 3ctj 3dkc 3dkf 3dkg 3efj 3efk 3f66 3f82 3i5n 3l8v 3lq8 3q6u 3q6w 3qti 3r7o 3rhk 3u6h 3u6i 3vw8 3zbx 3zc5 3zcl 3zxz 3zze 4aoi 4ap7 4deg 4deh 4dei 4eev 4gg5 4gg7 4iwd 4k3j 4knb 4mxc 4o3t 4o3u 4r1v 4r1y 4xmo 4xyf 5dg5 5eob 5eyc 5eyd 5hlw 5hni 5ho6 5hoa 5hor 5hti 5t3q 5uab 5uad 5uaf

(-) Related Entries Specified in the PDB File

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1r0p CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THEHEPATOCYTE GROWTH FACTOR RECEPTOR C-MET IN COMPLEX WITHTHE MICROBIAL ALKALOID K-252A
1r1w CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THEHEPATOCYTE GROWTH FACTOR RECEPTOR C-MET
1shy THE CRYSTAL STRUCTURE OF HGF BETA-CHAIN IN COMPLEX WITH THESEMA DOMAIN OF THE MET RECEPTOR.
1ssl SOLUTION STRUCTURE OF THE PSI DOMAIN FROM THE MET RECEPTOR
1ux3 3D STRUCTURE PREDICTION OF AMINO ACIDS 25 TO 656 OF HUMAN HEPATOCYTE GROWTH FACTOR/ SCATTER FACTOR (MET) RECEPTOR