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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 BOUND TO NOVEL BOSUTINIB ISOFORM 1, PREVIOUSLY THOUGHT TO BE BOSUTINIB
 
Authors :  M. Vollmar, M. Szklarz, A. Chaikuad, J. Elkins, P. Savitsky, K. A. Azeez T. Krojer, P. Canning, J. R. C. Muniz, C. Bountra, C. H. Arrowsmith, F. V J. Weigelt, A. Edwards, S. Knapp
Date :  01 Oct 12  (Deposition) - 10 Oct 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vollmar, M. Szklarz, A. Chaikuad, J. Elkins, P. Savitsky, K. A. Azeez, E. Salah, T. Krojer, P. Canning, J. R. C. Muniz, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, S. Knapp
Crystal Structure Of Human Serine Threonine Kinase- 10 Bound To Novel Bosutinib Isoform 1, Previously Thought To Be Bosutinib
To Be Published
PubMed: search

(-) 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
    Expression System VariantR3-LAMBDA-PPASE
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, RESIDUES 24-316
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE THREONINE KINASE-10, LYMPHOCYTE-ORIENTED KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2XZN1Ligand/Ion4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2XZN2Ligand/Ion4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:42 , ALA A:63 , LYS A:65 , GLU A:81 , VAL A:94 , ILE A:108 , ILE A:110 , GLU A:111 , PHE A:112 , CYS A:113 , PRO A:114 , GLU A:124 , LEU A:164 , ASP A:175 , HOH A:2035BINDING SITE FOR RESIDUE XZN A1317
2AC2SOFTWARETHR A:130 , PRO A:132 , GLN A:133 , ALA A:302 , GLU A:305 , HOH A:2044BINDING SITE FOR RESIDUE EDO A1318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BC6)

(-) 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:24-5229
1.2aENST000001767632aENSE00000769446chr5:171583792-171583628165STK10_HUMAN53-107551A:53-10755
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:291-31626
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
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   
          STK10_HUMAN    24 EHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVME 316
               SCOP domains d4bc6a_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...hhhh.eeeeeeee......eeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..hhhhhhhhhh..--------....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhh.hhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--------E--------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:24-52       Exon 1.2a  PDB: A:53-107 UniProt: 53-107               Exon 1.3         -------------------------------------------------Exon 1.7d                ----------------------------------------------------------------Exon 1.9b  PDB: A:263-290   Exon 1.10b  PDB: A:291-316 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)
                 4bc6 A  24 EHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQ--------PYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVME 316
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   |     -  |    203       213       223       233       243       253       263       273       283       293       303       313   
                                                                                                                                                                                             187      196                                                                                                                        

   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  (0, 0)

(no "CATH Domain" information available for 4BC6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BC6)

(-) 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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 Related Entries

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

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        STK10_HUMAN | O948042j7t 4aot 4equ 4usd 4use 5ajq

(-) Related Entries Specified in the PDB File

2j7t CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 BOUND TO SU11274
4aot CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 ( LOK) BOUND TO GW830263A