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(-) Description

Title :  INHIBITOR COMPLEX OF JNK3
 
Authors :  Y. Xue
Date :  08 Nov 05  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  X
Keywords :  Enzyme-Inhibitor Complex, Kinase Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. -M. Swahn, Y. Xue, E. Arzel, E. Kallin, A. Magnus, N. Plobeck, J. Viklund
Inhibitor Complex Of Jnk3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 10
    ChainsX
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneMAPK10, JNK3, JNK3A, PRKM10
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTRESS-ACTIVATED PROTEIN KINASE JNK3, C-JUN N- TERMINAL KINASE 3, MAP KINASE P49 3F12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1JNK1Ligand/IonN-{2'-[(4-FLUOROPHENYL)AMINO]-4,4'-BIPYRIDIN-2-YL}-4-METHOXYCYCLOHEXANECARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE X:70 , VAL X:78 , ALA X:91 , LYS X:93 , ILE X:124 , LEU X:126 , LEU X:144 , VAL X:145 , MET X:146 , MET X:149 , ASP X:150 , GLN X:155 , LEU X:206BINDING SITE FOR RESIDUE JNK X 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAPKPS01351 MAP kinase signature.MK10_HUMAN99-201  1X:99-201
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK10_HUMAN185-197  1X:185-197

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6bENST000003951696bENSE00002029030chr4:87281269-87280811459MK10_HUMAN-00--
1.11cENST0000039516911cENSE00001352600chr4:87275797-87275683115MK10_HUMAN-00--
1.14cENST0000039516914cENSE00001520792chr4:87115560-8711546299MK10_HUMAN-00--
1.17dENST0000039516917dENSE00002157878chr4:87080620-87080451170MK10_HUMAN1-41410--
1.19gENST0000039516919gENSE00002201403chr4:87028505-87028376130MK10_HUMAN41-84441X:45-84 (gaps)40
1.20bENST0000039516920bENSE00001800335chr4:87024397-8702433959MK10_HUMAN85-104201X:85-10420
1.21bENST0000039516921bENSE00001654569chr4:87023185-87023047139MK10_HUMAN104-150471X:104-15047
1.22bENST0000039516922bENSE00001609893chr4:87022370-87022205166MK10_HUMAN151-206561X:151-20656
1.23cENST0000039516923cENSE00001789401chr4:87019748-8701967772MK10_HUMAN206-230251X:206-230 (gaps)25
1.28bENST0000039516928bENSE00000729500chr4:86989108-86988926183MK10_HUMAN230-291621X:230-29162
1.29ENST0000039516929ENSE00000729498chr4:86985543-86985419125MK10_HUMAN291-332421X:291-33242
1.30ENST0000039516930ENSE00001076721chr4:86952584-8695252164MK10_HUMAN333-354221X:333-35422
1.31ENST0000039516931ENSE00001218615chr4:86950427-8695035078MK10_HUMAN354-380271X:354-380 (gaps)27
1.32hENST0000039516932hENSE00001811960chr4:86938523-869362762248MK10_HUMAN380-426471X:380-40021

(-) 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 X from PDB  Type:PROTEIN  Length:335
 aligned with MK10_HUMAN | P53779 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:356
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394      
           MK10_HUMAN    45 DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMN 400
               SCOP domains d2excx_ X: c-jun N-terminal    kinase (jnk3s)                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---2excX01 X:48-150 Phosphor   ylase Kinase; domain 1                                                     2excX02 X:151-370 Transferase(Phosphotransferase) domain 1                                                                                                                                                                  ---     ---------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeeeeee.---.eeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhh.........eeeee...........eeeeee...eehhhhh....hhhhhhhhhhhhhhhhhhhhh........hhh.eee.....eee......-------------......hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.......hhhhhh........hhhhhhhhhhhhhhhhhhh........hhhhhh....hhhhhhhhhhh....-----.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------MAPK  PDB: X:99-201 UniProt: 99-201                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.19g  PDB: X:45-84 (gaps)         Exon 1.20b          ----------------------------------------------Exon 1.22b  PDB: X:151-206 UniProt: 151-206             -----------------------Exon 1.28b  PDB: X:230-291 UniProt: 230-291                   -----------------------------------------Exon 1.30             -------------------------Exon 1.32h            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.21b  PDB: X:104-150 UniProt: 104-150    -------------------------------------------------------Exon 1.23c               ------------------------------------------------------------Exon 1.29  PDB: X:291-332 UniProt: 291-332---------------------Exon 1.31 UniProt: 354-380 -------------------- Transcript 1 (2)
                 2exc X  45 DNQFYSVEVGDSTFTVLKRYQNLKPIGS---GIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLA-------------VTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN 400
                                    54        64       | - |      84        94       104       114       124       134       144       154       164       174       184       194       204      |  -         -|      234       244       254       264       274       284       294       304       314       324       334       344       354       364        |-    |  384       394      
                                                      72  76                                                                                                                                    211           225                                                                                                                                                 373   379                     

   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 2EXC)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (MK10_HUMAN | P53779)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004705    JUN kinase activity    Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors.
    GO:0004707    MAP kinase activity    Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
    GO:0004708    MAP kinase kinase activity    Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate.
    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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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.
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007258    JUN phosphorylation    The process of introducing a phosphate group into a JUN protein.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0051090    regulation of sequence-specific DNA binding transcription factor activity    Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0009416    response to light stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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
        MK10_HUMAN | P537791jnk 1pmn 1pmu 1pmv 2b1p 2o0u 2o2u 2ok1 2p33 2r9s 2waj 2zdt 2zdu 3cgf 3cgo 3da6 3fi2 3fi3 3fv8 3g90 3g9l 3g9n 3kvx 3oxi 3oy1 3ptg 3rtp 3tti 3ttj 3v6r 3v6s 4h36 4h39 4h3b 4kke 4kkg 4kkh 4u79 4w4v 4w4w 4w4x 4w4y 4whz 4x21 4y46 4y5h 4z9l

(-) Related Entries Specified in the PDB File

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