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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 (LOK) BOUND TO GW830263A
 
Authors :  J. M. Elkins, E. Salah, M. Szklarz, P. Canning, F. Von Delft, W. Yue, Y. L C. Bountra, C. Arrowsmith, A. Edwards, S. Knapp
Date :  29 Mar 12  (Deposition) - 11 Apr 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Stk10, Lok (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Elkins, E. Salah, M. Szklarz, P. Canning, F. Von Delft, W. Yue, Y. Liu, C. Bountra, C. Arrowsmith, A. Edwards, S. Knapp
Crystal Structure Of Human Serine Threonine Kinase-10 (Lok) Bound To Gw830263A
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GW82Ligand/Ion1-(4-{METHYL[2-({4-[(METHYLSULFONYL)METHYL]PHENYL}AMINO)PYRIMIDIN-4-YL]AMINO}PHENYL)-3-{3-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]PHENYL}UREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GW81Ligand/Ion1-(4-{METHYL[2-({4-[(METHYLSULFONYL)METHYL]PHENYL}AMINO)PYRIMIDIN-4-YL]AMINO}PHENYL)-3-{3-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]PHENYL}UREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GW81Ligand/Ion1-(4-{METHYL[2-({4-[(METHYLSULFONYL)METHYL]PHENYL}AMINO)PYRIMIDIN-4-YL]AMINO}PHENYL)-3-{3-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]PHENYL}UREA

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:244 , LYS A:248BINDING SITE FOR RESIDUE CL A1315
2AC2SOFTWARELYS A:217BINDING SITE FOR RESIDUE CL A1316
3AC3SOFTWAREHOH A:2069BINDING SITE FOR RESIDUE CL A1317
4AC4SOFTWAREARG B:244BINDING SITE FOR RESIDUE CL B1316
5AC5SOFTWARETYR A:100BINDING SITE FOR RESIDUE CL A1318
6AC6SOFTWARELEU A:42 , ALA A:63 , LYS A:65 , TYR A:78 , ILE A:108 , ILE A:110 , GLU A:111 , PHE A:112 , CYS A:113 , ALA A:117 , ALA A:120 , LEU A:164 , ASP A:175 , PHE A:176 , HOH A:2026BINDING SITE FOR RESIDUE GW8 A1319
7AC7SOFTWARELEU B:42 , ALA B:63 , LYS B:65 , ILE B:67 , TYR B:78 , ILE B:108 , ILE B:110 , GLU B:111 , PHE B:112 , CYS B:113 , LEU B:164 , ASP B:175 , PHE B:176BINDING SITE FOR RESIDUE GW8 B1319

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AOT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041131R268CSTK10_HUMANPolymorphism35826078A/BR268C
2UniProtVAR_023827K277ESTK10_HUMANDisease (TGCT)757545210A/BK277E

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

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041131R268CSTK10_HUMANPolymorphism35826078BR268C
2UniProtVAR_023827K277ESTK10_HUMANDisease (TGCT)757545210BK277E

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

(-) PROSITE Motifs  (2, 4)

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

(-) Exons   (8, 16)

Asymmetric Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000001767631ENSE00000812846chr5:171615390-171614891500STK10_HUMAN1-52522A:16-52
B:16-52 (gaps)
37
37
1.2aENST000001767632aENSE00000769446chr5:171583792-171583628165STK10_HUMAN53-107552A:53-107
B:53-107
55
55
1.3ENST000001767633ENSE00000769445chr5:171554425-17155437749STK10_HUMAN108-124172A:108-124
B:108-124
17
17
1.4ENST000001767634ENSE00001003616chr5:171544634-171544485150STK10_HUMAN124-174512A:124-174
B:124-174
51
51
1.7dENST000001767637dENSE00001165742chr5:171534856-17153478473STK10_HUMAN174-198252A:174-198 (gaps)
B:174-198 (gaps)
25
25
1.8eENST000001767638eENSE00001165735chr5:171533818-171533624195STK10_HUMAN198-263662A:198-263 (gaps)
B:198-263 (gaps)
66
66
1.9bENST000001767639bENSE00000441213chr5:171532741-17153266082STK10_HUMAN263-290282A:263-290
B:263-290
28
28
1.10bENST0000017676310bENSE00000973051chr5:171523564-171523430135STK10_HUMAN291-335452A:291-314
B:291-314
24
24
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:278
 aligned with STK10_HUMAN | O94804 from UniProtKB/Swiss-Prot  Length:968

    Alignment length:299
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
          STK10_HUMAN    16 EKRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEV 314
               SCOP domains d4aota_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..hhhh.eeeeeeeee....eeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.......-------------......hhhhhh--------..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhh..........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--------E------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:16-52 UniProt: 1-52 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 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:124-174 UniProt: 124-174          -----------------------Exon 1.8e  PDB: A:198-263 (gaps) UniProt: 198-263                 --------------------------------------------------- Transcript 1 (2)
                 4aot A  16 SMRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSA-------------GTPYWMAPEVVM--------YDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEV 314
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    |    -       195       205       215       225       235       245       255       265       275       285       295       305         
                                                                                                                                                                                              180           194        205      214                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with STK10_HUMAN | O94804 from UniProtKB/Swiss-Prot  Length:968

    Alignment length:299
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
          STK10_HUMAN    16 EKRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEV 314
               SCOP domains d4aotb_ B: au  tomated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......ee.--hhhh.eeeeeeeee....eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee........-----------.......hhhhhh-------...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhh..........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--------E------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:16-52 (gaps)        Exon 1.2a  PDB: B:53-107 UniProt: 53-107               Exon 1.3         -------------------------------------------------Exon 1.7d                ----------------------------------------------------------------Exon 1.9b  PDB: B:263-290   Exon 1.10b [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:124-174 UniProt: 124-174          -----------------------Exon 1.8e  PDB: B:198-263 (gaps) UniProt: 198-263                 --------------------------------------------------- Transcript 1 (2)
                 4aot B  16 SMRKSREYEHVRR--DPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAK-----------IGTPYWMAPEVVM-------PYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEV 314
                                    25  |  |  35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     |   -       195       205       215       225       235       245       255       265       275       285       295       305         
                                       28 31                                                                                                                                                   181         193         205     213                                                                                                     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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)

UniProtKB/Swiss-Prot
        STK10_HUMAN | O948042j7t 4bc6 4equ 4usd 4use 5ajq

(-) Related Entries Specified in the PDB File

2j7t CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 BOUND TO SU11274
3zz2 CRYSTAL STRUCTURE OF HUMAN SERINE THREONINE KINASE-10 BOUND TO 4-[(2,4-DICHLORO-5-METHOXYPHENYL)AMINO]-6 - METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY] QUINOLINE-3-CARBONITRILE APPARENTLY MODIFIED THROUGH RADIATION DAMAGE