Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HUMAN EPHA3 KINASE AND JUXTAMEMBRANE REGION BOUND TO SUBSTRATE KQWDNYE[PTYR]IW
 
Authors :  T. Davis, J. R. Walker, F. Mackenzie, J. Weigelt, C. Bountra, C. H. Arrow A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics C (Sgc)
Date :  21 Jan 09  (Deposition) - 03 Feb 09  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor Tyrosine Kinase, Juxtamembrane Segment, Structural Genomics, Peptide Co-Crystal Structure, Substrate Complex, Structural Genomics Consortium, Sgc, Atp-Binding, Cell Membrane, Glycoprotein, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Receptor, Secreted, Transferase, Transmembrane, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. L. Davis, J. R. Walker, A. Allali-Hassani, S. A. Parker, B. E. Turk, S. Dhe-Paganon
Structural Recognition Of An Optimized Substrate For The Ephrin Family Of Receptor Tyrosine Kinases.
Febs J. V. 276 4395 2009
PubMed-ID: 19678838  |  Reference-DOI: 10.1111/J.1742-4658.2009.07147.X

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 3
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentJUXTAMEMBRANE SEGMENT AND KINASE DOMAIN: RESIDUES 577-947
    GeneEPHA3, ETK, ETK1, HEK, TYRO4
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR ETK1, HEK, HEK4, TYROSINE- PROTEIN KINASE TYRO4
 
Molecule 2 - PEPTIDE SUBSTRATE
    ChainsB
    EngineeredYES
    Other DetailsPEPTIDE SYNTHESIZED WITH PHOSPHORYLATION AT THE +2 TYROSINE POSITION
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:81 , HOH A:154 , HOH A:301 , ANP A:992BINDING SITE FOR RESIDUE MG A 991
2AC2SOFTWAREHOH A:8 , HOH A:17 , HOH A:48 , HOH A:76 , HOH A:81 , HOH A:94 , HOH A:154 , HOH A:301 , ALA A:629 , GLY A:630 , GLU A:631 , ALA A:651 , THR A:699 , GLU A:700 , TYR A:701 , MET A:702 , SER A:706 , LEU A:753 , MG A:991BINDING SITE FOR RESIDUE ANP A 992

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FXX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:693 -Pro A:694

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036088I621LEPHA3_HUMANUnclassified  ---AI621L
2CancerSNPVAR_EPHA3_HUMAN_CCDS2922_1_03 *I621LEPHA3_HUMANDisease (Colorectal cancer)  ---AI621L
3UniProtVAR_065831T660KEPHA3_HUMANUnclassified  ---AT660K
4UniProtVAR_042132G766EEPHA3_HUMANUnclassified  ---AG766E
5UniProtVAR_036089D806NEPHA3_HUMANUnclassified  ---AD806N
6CancerSNPVAR_EPHA3_HUMAN_CCDS2922_1_04 *D806NEPHA3_HUMANDisease (Colorectal cancer)  ---AD806N
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHA3_HUMAN627-653  1A:627-653
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA3_HUMAN742-754  1A:742-754

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003365961aENSE00001330937chr3:89156674-89156986313EPHA3_HUMAN1-30300--
1.2ENST000003365962ENSE00001309114chr3:89176359-8917642365EPHA3_HUMAN30-51220--
1.3ENST000003365963ENSE00001329887chr3:89259010-89259670661EPHA3_HUMAN52-2722210--
1.4ENST000003365964ENSE00001157881chr3:89390066-89390221156EPHA3_HUMAN272-324530--
1.5ENST000003365965ENSE00000774362chr3:89390905-89391240336EPHA3_HUMAN324-4361130--
1.6ENST000003365966ENSE00001000999chr3:89444987-89445111125EPHA3_HUMAN436-477420--
1.7aENST000003365967aENSE00000774379chr3:89448468-89448630163EPHA3_HUMAN478-532550--
1.8ENST000003365968ENSE00000774381chr3:89456419-89456521103EPHA3_HUMAN532-566350--
1.9ENST000003365969ENSE00000774382chr3:89457217-8945728165EPHA3_HUMAN566-588230--
1.10ENST0000033659610ENSE00000774383chr3:89462291-89462416126EPHA3_HUMAN588-630431A:606-63025
1.11ENST0000033659611ENSE00000774387chr3:89468355-89468540186EPHA3_HUMAN630-692631A:630-69263
1.12ENST0000033659612ENSE00000774392chr3:89478256-8947831762EPHA3_HUMAN692-712211A:692-71221
1.13ENST0000033659613ENSE00000774396chr3:89480300-89480509210EPHA3_HUMAN713-782701A:713-77462
1.14ENST0000033659614ENSE00001744925chr3:89498375-89498524150EPHA3_HUMAN783-832501A:784-83249
1.15ENST0000033659615ENSE00001142474chr3:89499327-89499520194EPHA3_HUMAN833-897651A:833-897 (gaps)65
1.16bENST0000033659616bENSE00001142467chr3:89521614-89521769156EPHA3_HUMAN897-949531A:897-9048
1.17bENST0000033659617bENSE00001353258chr3:89528547-895312842738EPHA3_HUMAN949-983350--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:288
 aligned with EPHA3_HUMAN | P29320 from UniProtKB/Swiss-Prot  Length:983

    Alignment length:299
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895         
          EPHA3_HUMAN   606 TQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSNLLLD 904
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fxxA01 A:606-702 Phosphorylase Kinase; domain 1                                                 3fxxA02 A:703-904 Transferase(Phosphotransferase) domain 1                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....hhh.eeeeeeeee....eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee....---------...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhee.......hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh..--.......ee. Sec.struct. author
             SAPs(SNPs) (1) ---------------L--------------------------------------K---------------------------------------------------------------------------------------------------------E---------------------------------------N-------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:606-630-------------------------------------------------------------Exon 1.12            Exon 1.13  PDB: A:713-774 UniProt: 713-782 [INCOMPLETE]               Exon 1.14  PDB: A:784-832 UniProt: 783-832        Exon 1.15  PDB: A:833-897 (gaps) UniProt: 833-897                ------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.11  PDB: A:630-692 UniProt: 630-692                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1.16b    Transcript 1 (2)
                 3fxx A 606 TQTVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDD---------GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIIT--AARPSNLLLD 904
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765        |-       785       795       805       815       825       835       845       855       865       875       885      |895         
                                                                                                                                                                                                  774       784                                                                                                         892  |         
                                                                                                                                                                                                                                                                                                                           895         

Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3fxx B  -4 QWDNYEyIW   4
                                  |  
                                  2-PTR

   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 3FXX)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FXX)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EPHA3_HUMAN | P29320)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005004    GPI-linked ephrin receptor activity    Combining with a GPI-anchored ephrin to initiate a change in cell activity.
    GO:0005003    ephrin receptor activity    Combining with an ephrin 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: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: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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0097156    fasciculation of motor neuron axon    The collection of motor neuron axons into a bundle of rods, known as a fascicle.
    GO:0097155    fasciculation of sensory neuron axon    The collection of sensory neuron axons into a bundle of rods, known as a fascicle.
    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:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0010717    regulation of epithelial to mesenchymal transition    Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0051893    regulation of focal adhesion assembly    Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
    GO:0070507    regulation of microtubule cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:693 - Pro A:694   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3fxx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EPHA3_HUMAN | P29320
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  EPHA3_HUMAN | P29320
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA3_HUMAN | P293202gsf 2qo2 2qo7 2qo9 2qob 2qoc 2qod 2qof 2qoi 2qok 2qol 2qon 2qoo 2qoq 3dzq 3fy2 4g2f 4gk2 4gk3 4gk4 4l0p 4p4c 4p5q 4p5z 4twn 4two

(-) Related Entries Specified in the PDB File

1ir3 INSULIN RECEPTOR KINASE COMPLEXED WITH SUBSTRATE
2gsf APO FORM OF HUMAN EPHA3 RECEPTOR TYROSINE KINASE AND JUXTAMEMBRANE REGION
2qoc ACTIVE FORM OF HUMAN EPHA3 RECEPTOR TYROSINE KINASE AND JUXTAMEMBRANE REGION
3fy2 HUMAN EPHA3 KINASE AND JUXTAMEMBRANE REGION BOUND TO SUBSTRATE KQWDNYEFIW