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(-) Description

Title :  COMPLEX BETWEEN THE KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 7 (EPHA7) AND INHIBITOR ALW-II-49-7
 
Authors :  J. R. Walker, F. Syeda, N. Gray, C. Butler-Cole, C. Bountra, M. Wolkstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe- Paganon, Structural Genomics Consortium (Sgc)
Date :  25 Jun 08  (Deposition) - 19 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding, Kinase, Nucleotide-Binding, Receptor, Signal, Transferase, Phosphorylation, Transmembrane, Tyrosine- Protein Kinase, Alternative Splicing, Glycoprotein, Inhibitor, Structural Genomics Consortium, Sgc, Membrane, Phosphoprotein, Polymorphism, Nppsfa, National Project On Protein Structural And Functional Analyses (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, F. Syeda, N. Gray, C. Butler-Cole, C. Bountra, M. Wolkstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Kinase Domain Of Human Ephrin Type-A Receptor 7 (Epha7) In Complex With Alw-Ii-49-7
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 7
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CH
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, UNP RESIDUES 590-899
    GeneEPHA7, EHK3, HEK11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR EHK-3, EPH HOMOLOGY KINASE 3, RECEPTOR PROTEIN-TYROSINE KINASE HEK11
    TissueBRAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IHZ1Ligand/Ion5-[(2-METHYL-5-{[3-(TRIFLUOROMETHYL)PHENYL]CARBAMOYL}PHENYL)AMINO]PYRIDINE-3-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:663 , GLU A:682 , MET A:686 , PHE A:689 , ILE A:711 , GLU A:712 , MET A:714 , TYR A:754 , LEU A:765 , SER A:775 , ASP A:776 , PHE A:777 , HOH A:1133BINDING SITE FOR RESIDUE IHZ A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DKO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DKO)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.EPHA7_HUMAN639-665  1A:639-665
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.EPHA7_HUMAN754-766  1A:754-766

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003693031cENSE00001941413chr6:94129244-94128963282EPHA7_HUMAN1-33330--
1.2ENST000003693032ENSE00000974737chr6:94124485-9412442165EPHA7_HUMAN33-54220--
1.3aENST000003693033aENSE00000918734chr6:94120888-94120219670EPHA7_HUMAN55-2782240--
1.4ENST000003693034ENSE00000974738chr6:94068129-94067974156EPHA7_HUMAN278-330530--
1.5ENST000003693035ENSE00000974739chr6:94066770-94066435336EPHA7_HUMAN330-4421130--
1.6ENST000003693036ENSE00001309196chr6:93982140-93982016125EPHA7_HUMAN442-483420--
1.7bENST000003693037bENSE00000974741chr6:93979378-93979195184EPHA7_HUMAN484-545620--
1.8ENST000003693038ENSE00001084117chr6:93974420-93974312109EPHA7_HUMAN545-581370--
1.9ENST000003693039ENSE00000974743chr6:93973633-9397357856EPHA7_HUMAN581-600200--
1.10ENST0000036930310ENSE00000974744chr6:93969197-93969072126EPHA7_HUMAN600-642431A:607-64135
1.11ENST0000036930311ENSE00000974745chr6:93968002-93967817186EPHA7_HUMAN642-704631A:643-70462
1.12ENST0000036930312ENSE00000974746chr6:93967241-9396718062EPHA7_HUMAN704-724211A:704-72421
1.13ENST0000036930313ENSE00002150360chr6:93965755-93965546210EPHA7_HUMAN725-794701A:725-77854
1.14ENST0000036930314ENSE00002154876chr6:93964514-93964365150EPHA7_HUMAN795-844501A:799-84446
1.15ENST0000036930315ENSE00000974749chr6:93956703-93956510194EPHA7_HUMAN845-909651A:845-90258
1.16ENST0000036930316ENSE00000974750chr6:93955171-93955016156EPHA7_HUMAN909-961530--
1.17ENST0000036930317ENSE00001449448chr6:93953258-939497383521EPHA7_HUMAN961-998380--

(-) 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:275
 aligned with EPHA7_HUMAN | Q15375 from UniProtKB/Swiss-Prot  Length:998

    Alignment length:296
                                   616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896      
          EPHA7_HUMAN   607 TYIDPETYEDPNRAVHQFAKELDASCIKIERVIGAGEFGEVCSGRLKLPGKRDVAVAIKTLKVGYTEKQRRDFLCEASIMGQFDHPNVVHLEGVVTRGKPVMIVIEFMENGALDAFLRKHDGQFTVIQLVGMLRGIAAGMRYLADMGYVHRDLAARNILVNSNLVCKVSDFGLSRVIEDDPEAVYTTTGGKIPVRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVIKAIEEGYRLPAPMDCPAGLHQLMLDCWQKERAERPKFEQIVGILDKMIRNPNSLKT 902
               SCOP domains d3dkoa_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3dkoA01 A:607-713 Phosphorylase Kin ase; domain 1                                                          3dkoA02 A:714-902 Transferase(Phosphotransferase) domain 1                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.hhhhhhhhhh...hhh.eeeeeeee.-....eeeeee.......eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....--------------------hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:607-641           -------------------------------------------------------------Exon 1.12            Exon 1.13  PDB: A:725-778 UniProt: 725-794 [INCOMPLETE]               Exon 1.14  PDB: A:799-844 UniProt: 795-844        Exon 1.15  PDB: A:845-902 UniProt: 845-909 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.11  PDB: A:643-704 UniProt: 642-704 [INCOMPLETE]        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dko A 607 TYIDPETYEDPNRAVHQFAKELDASCIKIERVIGA-EFGEVCSGRLKLPGKRDVAVAIKTLKVGYTEKQRRDFLCEASIMGQFDHPNVVHLEGVVTRGKPVMIVIEFMENGALDAFLRKHDGQFTVIQLVGMLRGIAAGMRYLADMGYVHRDLAARNILVNSNLVCKVSDFG--------------------PVRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVIKAIEEGYRLPAPMDCPAGLHQLMLDCWQKERAERPKFEQIVGILDKMIRNPNSAHH 902
                                   616       626       636    | |646       656       666       676       686       696       706       716       726       736       746       756       766       776 |       -         -  |    806       816       826       836       846       856       866       876       886       896      
                                                            641 |                                                                                                                                    778                  799                                                                                                       
                                                              643                                                                                                                                                                                                                                                                   

   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  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EPHA7_HUMAN | Q15375)
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:0008046    axon guidance receptor activity    Combining with an extracellular messenger and transmitting the signal from one side of the membrane to the other to results in a change in cellular activity involved in axon guidance.
    GO:0045499    chemorepellent activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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: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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0048755    branching morphogenesis of a nerve    The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron).
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0050919    negative chemotaxis    The directed movement of a motile cell or organism towards a lower concentration of a chemical.
    GO:0048671    negative regulation of collateral sprouting    Any process that stops, prevents, or reduces the frequency, rate or extent of collateral sprouting.
    GO:0051964    negative regulation of synapse assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0072178    nephric duct morphogenesis    The process in which the anatomical structures of the nephric duct are generated and organized. A nephric duct is a tube that drains a primitive kidney.
    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: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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0070372    regulation of ERK1 and ERK2 cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0022407    regulation of cell-cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell.
    GO:0043281    regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.
    GO:0050730    regulation of peptidyl-tyrosine phosphorylation    Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0031952    regulation of protein autophosphorylation    Any process that modulates the frequency, rate or extent of addition of the phosphorylation by a protein of one or more of its own residues.
    GO:0031290    retinal ganglion cell axon guidance    The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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: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: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:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA7_HUMAN | Q153752rei 3h8m 3nru

(-) Related Entries Specified in the PDB File

2rei KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 7 (EPHA7)