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

(-) Description

Title :  KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 5 (EPHA5)
 
Authors :  J. R. Walker, D. Cuerrier, C. Butler-Cole, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
Date :  27 Aug 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding, Kinase, Nucleotide-Binding, Receptor, Signal, Transferase, Phosphorylation, Transmembrane, Tyrosine- Protein Kinase, Alternative Splicing, Glycoprotein, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, D. Cuerrier, C. Butler-Cole, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Kinase Domain Of Human Ephrin Type-A Receptor 5 (Epha5).
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 5
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC-CH
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN: RESIDUES 653-939
    GeneEPHA5, EHK1, HEK7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR EHK-1, EPH HOMOLOGY KINASE 1, RECEPTOR PROTEIN-TYROSINE KINASE HEK7

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2R2P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R2P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:747 -Pro A:748

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042144A672TEPHA5_HUMANPolymorphism36050417AA672T
2UniProtVAR_042145S673TEPHA5_HUMANPolymorphism56359290AS673T
3UniProtVAR_042146T856IEPHA5_HUMANUnclassified  ---AT856I
4UniProtVAR_042147H959REPHA5_HUMANPolymorphism56312931AH942R

  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.EPHA5_HUMAN681-707  1A:681-707
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA5_HUMAN796-808  1A:796-808

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002738541bENSE00001816165chr4:66536061-66535280782EPHA5_HUMAN1-61610--
1.2ENST000002738542ENSE00001139193chr4:66509145-6650908165EPHA5_HUMAN61-82220--
1.3ENST000002738543ENSE00001139187chr4:66468022-66467359664EPHA5_HUMAN83-3042220--
1.4ENST000002738544ENSE00001139210chr4:66361261-66361106156EPHA5_HUMAN304-356530--
1.5ENST000002738545ENSE00001139204chr4:66356430-66356095336EPHA5_HUMAN356-4681130--
1.6ENST000002738546ENSE00001139296chr4:66286283-66286159125EPHA5_HUMAN468-509420--
1.7ENST000002738547ENSE00001139288chr4:66280161-66280002160EPHA5_HUMAN510-563540--
1.8bENST000002738548bENSE00001139282chr4:66270194-66270092103EPHA5_HUMAN563-597350--
1.9ENST000002738549ENSE00000969519chr4:66242781-6624271666EPHA5_HUMAN597-619230--
1.10ENST0000027385410ENSE00000969520chr4:66233142-6623307568EPHA5_HUMAN619-642240--
1.11ENST0000027385411ENSE00000969521chr4:66231775-66231650126EPHA5_HUMAN642-684431A:662-68423
1.12ENST0000027385412ENSE00000969522chr4:66230920-66230735186EPHA5_HUMAN684-746631A:684-74663
1.13ENST0000027385413ENSE00000969523chr4:66218821-6621876062EPHA5_HUMAN746-766211A:746-76621
1.14ENST0000027385414ENSE00000969524chr4:66217316-66217107210EPHA5_HUMAN767-836701A:767-836 (gaps)70
1.15ENST0000027385415ENSE00001631595chr4:66213921-66213772150EPHA5_HUMAN837-886501A:838-88649
1.16ENST0000027385416ENSE00000969526chr4:66201843-66201650194EPHA5_HUMAN887-951651A:887-93953
1.17aENST0000027385417aENSE00000969527chr4:66197846-66197691156EPHA5_HUMAN951-1003531A:940-9467
1.18cENST0000027385418cENSE00001634548chr4:66189937-661852814657EPHA5_HUMAN1003-1037350--

(-) 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:283
 aligned with EPHA5_HUMAN | P54756 from UniProtKB/Swiss-Prot  Length:1037

    Alignment length:302
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961  
          EPHA5_HUMAN   662 AVHEFAKEIEASCITIERVIGAGEFGEVCSGRLKLPGKRELPVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIHLEGVVTKSKPVMIVTEYMENGSLDTFLKKNDGQFTVIQLVGMLRGISAGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDDPEAAYTTRGGKIPIRWTAPEAIAFRKFTSASDVWSYGIVMWEVVSYGERPYWEMTNQDVIKAVEEGYRLPSPMDCPAALYQLMLDCWQKERNSRPKFDEIVNMLDKLIRNPSSLKTLVNASCRVSNLLAEHSPLG 963
               SCOP domains d2r2pa_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2r2pA01 A:662-755 Phosphorylase Kinase; domain 1                                              2r2pA02 A:756-946 Transferase(Phosphotransferase) domain 1                                                                                                                                                       CATH domains
               Pfam domains -------------Pkinase_Tyr-2r2pA01 A:675-932                                                                                                                                                                                                                                     -------                 ------- Pfam domains
         Sec.struct. author hhhhh....hhh.eeeeeeeee....eeeeeee.......eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....-..ee..-...hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh-----------------hhh.... Sec.struct. author
                 SAPs(SNPs) ----------TT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------R---- SAPs(SNPs)
                    PROSITE -------------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11 [INCOMPLETE] -------------------------------------------------------------Exon 1.13            Exon 1.14  PDB: A:767-836 (gaps) UniProt: 767-836                     Exon 1.15  PDB: A:838-886 UniProt: 837-886        Exon 1.16  PDB: A:887-939 UniProt: 887-951 [INCOMPLETE]          ------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.12  PDB: A:684-746 UniProt: 684-746                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17a    Transcript 1 (2)
                 2r2p A 662 AVHEFAKEIEASCITIERVIGAGEFGEVCSGRLKLPGKRELPVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIHLEGVVTKSKPVMIVTEYMENGSLDTFLKKNDGQFTVIQLVGMLRGISAGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDDP-AAYTTR-GKIPIRWTAPEAIAFRKFTSASDVWSYGIVMWEVVSYGERPYWEMTNQDVIKAVEEGYRLPSPMDCPAALYQLMLDCWQKERNSRPKFDEIVNMLDKLIRNP-----------------AHHHHHH 946
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831    | |841       851       861       871       881       891       901       911       921       931       | -         -     | 944  
                                                                                                                                                                                                 829 |  836 |                                                                                                  939               940      
                                                                                                                                                                                                   831    838                                                                                                                             

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EPHA5_HUMAN | P54756)
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: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.
    GO:0005005    transmembrane-ephrin receptor activity    Combining with a transmembrane ephrin to initiate a change in cell activity.
biological process
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    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:0032793    positive regulation of CREB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
    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:0061178    regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0005791    rough endoplasmic reticulum    The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2r2p)
 
  Cis Peptide Bonds
    Lys A:747 - Pro A:748   [ 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
  2r2p
    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
  EPHA5_HUMAN | P54756
    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
  EPHA5_HUMAN | P54756
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA5_HUMAN | P547564et7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2R2P)