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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 BOUND TO SU11274
 
Authors :  A. C. W. Pike, P. Rellos, O. Fedorov, S. Das, J. Debreczeni, F. Sobott, S. P. Savitsky, J. Eswaran, A. P. Turnbull, E. Papagrigoriou, E. Ugochuk F. Gorrec, C. C. Umeano, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. M. Sundstrom, S. Knapp
Date :  17 Oct 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kinase, Transferase, Atp-Binding, Cell Cycle Progression, Phosphorylation, Disease Mutation, Nucleotide- Binding, Lymphocyte Oriented Kinase (Lok), Serine/Threonine- Protein Kinase, Serine/Threonine Kinase (Stk10A) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. W. Pike, P. Rellos, F. H. Niesen, A. Turnbull, A. W. Oliver, S. A. Parker, B. E. Turk, L. H. Pearl, S. Knapp
Activation Segment Dimerization: A Mechanism For Kinase Autophosphorylation Of Non-Consensus Sites.
Embo J. V. 27 704 2008
PubMed-ID: 18239682  |  Reference-DOI: 10.1038/EMBOJ.2008.8

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE 10
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentKINASE DOMAIN, RESIDUES 18-317
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLYMPHOCYTE-ORIENTED KINASE, SERINE-THREONINE PROTEIN KINASE-10

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
12741Ligand/Ion(3Z)-N-(3-CHLOROPHENYL)-3-({3,5-DIMETHYL-4-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-1H-PYRROL-2-YL}METHYLENE)-N-METHYL-2-OXOINDOLINE-5-SULFONAMIDE
2ACT1Ligand/IonACETATE ION
3CA7Ligand/IonCALCIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12742Ligand/Ion(3Z)-N-(3-CHLOROPHENYL)-3-({3,5-DIMETHYL-4-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-1H-PYRROL-2-YL}METHYLENE)-N-METHYL-2-OXOINDOLINE-5-SULFONAMIDE
2ACT2Ligand/IonACETATE ION
3CA-1Ligand/IonCALCIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2013 , HOH A:2014 , HOH A:2016 , HOH A:2019 , HOH A:2058BINDING SITE FOR RESIDUE CA A 332
2AC2SOFTWAREHOH A:2020 , HOH A:2051 , HOH A:2059 , HOH A:2129 , HOH A:2130BINDING SITE FOR RESIDUE CA A 333
3AC3SOFTWAREGLU A:168 , GLU A:316 , HOH A:2054 , HOH A:2125 , HOH A:2127 , HOH A:2128BINDING SITE FOR RESIDUE CA A1318
4AC4SOFTWAREGLU A:313 , GLU A:316 , HOH A:2055 , HOH A:2128BINDING SITE FOR RESIDUE CA A1319
5AC5SOFTWAREGLU A:234 , HOH A:2078 , HOH A:2079 , HOH A:2080BINDING SITE FOR RESIDUE CA A1320
6AC6SOFTWAREGLN A:135 , HOH A:2039 , HOH A:2108BINDING SITE FOR RESIDUE CA A1321
7AC7SOFTWAREGLU A:124 , GLU A:313 , HOH A:2028 , HOH A:2126BINDING SITE FOR RESIDUE CA A1322
8AC8SOFTWARETHR A:298 , VAL A:314BINDING SITE FOR RESIDUE ACT A1323
9AC9SOFTWARELEU A:42 , ALA A:63 , GLU A:81 , ILE A:108 , ILE A:110 , GLU A:111 , PHE A:112 , CYS A:113 , GLY A:116 , ALA A:117 , LEU A:164 , ASP A:175 , HOH A:2007 , HOH A:2129BINDING SITE FOR RESIDUE 274 A1324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J7T)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:212 -Pro A:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041131R268CSTK10_HUMANPolymorphism35826078AR268C
2UniProtVAR_023827K277ESTK10_HUMANDisease (TGCT)757545210AK277E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041131R268CSTK10_HUMANPolymorphism35826078AR268C
2UniProtVAR_023827K277ESTK10_HUMANDisease (TGCT)757545210AK277E

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK10_HUMAN42-65  1A:42-65
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.STK10_HUMAN153-165  1A:153-165
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK10_HUMAN42-65  2A:42-65
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.STK10_HUMAN153-165  2A:153-165

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000001767631ENSE00000812846chr5:171615390-171614891500STK10_HUMAN1-52521A:25-5228
1.2aENST000001767632aENSE00000769446chr5:171583792-171583628165STK10_HUMAN53-107551A:53-107 (gaps)55
1.3ENST000001767633ENSE00000769445chr5:171554425-17155437749STK10_HUMAN108-124171A:108-12417
1.4ENST000001767634ENSE00001003616chr5:171544634-171544485150STK10_HUMAN124-174511A:124-17451
1.7dENST000001767637dENSE00001165742chr5:171534856-17153478473STK10_HUMAN174-198251A:174-198 (gaps)25
1.8eENST000001767638eENSE00001165735chr5:171533818-171533624195STK10_HUMAN198-263661A:198-26366
1.9bENST000001767639bENSE00000441213chr5:171532741-17153266082STK10_HUMAN263-290281A:263-29028
1.10bENST0000017676310bENSE00000973051chr5:171523564-171523430135STK10_HUMAN291-335451A:291-31727
1.11aENST0000017676311aENSE00000973052chr5:171520964-171520416549STK10_HUMAN336-5181830--
1.13ENST0000017676313ENSE00001507188chr5:171517366-171517236131STK10_HUMAN519-562440--
1.14ENST0000017676314ENSE00001507187chr5:171510088-171509965124STK10_HUMAN562-603420--
1.15aENST0000017676315aENSE00000973055chr5:171509509-171509330180STK10_HUMAN604-663600--
1.16aENST0000017676316aENSE00001003610chr5:171491816-17149172493STK10_HUMAN664-694310--
1.18cENST0000017676318cENSE00001003619chr5:171488272-171488143130STK10_HUMAN695-738440--
1.19bENST0000017676319bENSE00001084482chr5:171484477-171484353125STK10_HUMAN738-779420--
1.20bENST0000017676320bENSE00000973060chr5:171482780-171482592189STK10_HUMAN780-842630--
1.21ENST0000017676321ENSE00000973061chr5:171481698-171481573126STK10_HUMAN843-884420--
1.22bENST0000017676322bENSE00000973062chr5:171480046-171479933114STK10_HUMAN885-922380--
1.24cENST0000017676324cENSE00001003620chr5:171472026-1714690772950STK10_HUMAN923-968460--

(-) Sequences/Alignments

Asymmetric 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:285
 aligned with STK10_HUMAN | O94804 from UniProtKB/Swiss-Prot  Length:968

    Alignment length:293
                                    34        44        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   
          STK10_HUMAN    25 HVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEE 317
               SCOP domains d2j7ta_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2j7tA01 A:25-112 Phosphorylase Kinase; domai    n 1                                     2j7tA02 A:113-317 Transferase(Phosphotransferase) domain 1                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh.eeeeeeee......eeeeee.....eeeeeee.----.hhhhhhhhhhhhhhh.......eeeeee....eeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..hhhhhhhhhhhhh----..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhh..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--------E---------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:25-52      Exon 1.2a  PDB: A:53-107 (gaps) UniProt: 53-107        Exon 1.3         -------------------------------------------------Exon 1.7d                ----------------------------------------------------------------Exon 1.9b  PDB: A:263-290   Exon 1.10b  PDB: A:291-317  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:124-174 UniProt: 124-174          -----------------------Exon 1.8e  PDB: A:198-263 UniProt: 198-263                        ------------------------------------------------------ Transcript 1 (2)
                 2j7t A  25 HVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIE----EELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQK----IGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEE 317
                                    34        44        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   
                                                                      68   73                                                                                                                188  193                                                                                                                            

   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 Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J7T)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (STK10_HUMAN | O94804)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0042801    obsolete polo kinase kinase activity    OBSOLETE Catalysis of the addition of a phosphate group onto a serine or threonine residue in any member of the polo kinase class of proteins. This term was made obsolete because it represents a gene product and also refers to a non-existent activity (polo kinase).
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0071593    lymphocyte aggregation    The adhesion of one lymphocyte to one or more other lymphocytes via adhesion molecules.
    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:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:2000401    regulation of lymphocyte migration    Any process that modulates the frequency, rate or extent of lymphocyte migration.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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        STK10_HUMAN | O948044aot 4bc6 4equ 4usd 4use 5ajq

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