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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE 17B (STK17B)
 
Authors :  E. Ugochukwu, M. Soundararajan, P. Rellos, O. Fedorov, C. Phillips, J. E. Hapka, P. Filippakopoulos, A. Chaikuad, A. C. W. Pike, F. Von Delft C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp, Struct Genomics Consortium (Sgc)
Date :  29 Jan 10  (Deposition) - 16 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Stk17B, Serine/Threonine Kinase 17B, Drak2, Dap Kinase Related Apoptosis-Inducing Protein Kinase 2, Death-Associated Protein Kinase-Related 2, Structural Genomics, Structural Genomics Consortium, Sgc, Apoptosis, Atp-Binding, Kinase, Nucleotide-Binding, Nucleus, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  

PubMed: search

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE 17B
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid562
    GeneDRAK2, STK17B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDAP KINASE-RELATED APOPTOSIS-INDUCING PROTEIN KINASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EBD1Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]-5-METHYLPYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE
3EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECL A:2 , LYS A:37 , ALA A:60 , LYS A:62 , GLU A:111 , TYR A:112 , ALA A:113 , GLY A:116 , GLU A:117 , GLN A:162 , ASN A:163 , LEU A:165 , VAL A:178 , ASP A:179 , HOH A:457BINDING SITE FOR RESIDUE EBD A 1
2AC2SOFTWAREVAL A:46 , ARG A:48 , PHE A:63 , GLU A:132 , SER A:263 , HOH A:344 , HOH A:403BINDING SITE FOR RESIDUE EDO A 330
3AC3SOFTWAREEBD A:1 , ASP A:179BINDING SITE FOR RESIDUE CL A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LM0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:170 -Pro A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LM0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ST17B_HUMAN39-62  1A:39-62
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.ST17B_HUMAN154-166  1A:154-166

(-) Exons   (0, 0)

(no "Exon" information available for 3LM0)

(-) 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:278
 aligned with ST17B_HUMAN | O94768 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:293
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
          ST17B_HUMAN    12 SGLLTTTPQIPIKMENFNNFYILTSKELGRGKFAVVRQCISKSTGQEYAAKFLKKRRRGQDCRAEILHEIAVLELAKSCPRVINLHEVYENTSEIILILEYAAGGEIFSLCLPELAEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKIGHACELREIMGTPEYLAPEILNYDPITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQVNVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLSHSWLQQWDFENLFHP 304
               SCOP domains d3lm0a_       A: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------      --------Pkinase-3lm0A01 A:33-293                                                                                                                                                                                                                                             ----------- Pfam domains
         Sec.struct. author ......h------hhhhhhheeeeeeeeee...eeeeeeee.....eeeeeeee.ee..eehhhhhhhhhhhhhhh........eeeeee...eeeeeee....ee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee.........---------..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lm0 A  18 ENLYFQS------MENFNNFYILTSKELGRGKFAVVRQCISKSTGQEYAAKFLKKRRRGQDCRAEILHEIAVLELAKSCPRVINLHEVYENTSEIILILEYAAGGEIFSLCLPELAEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKI---------MGTPEYLAPEILNYDPITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQVNVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLSHSWLQQWDFENLFHP 304
                                  |  -   |    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    |    -    |  201       211       221       231       241       251       261       271       281       291       301   
                                 24     25                                                                                                                                                              186       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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LM0)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ST17B_HUMAN | O94768)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    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:2000271    positive regulation of fibroblast apoptotic process    Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    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.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        ST17B_HUMAN | O947683lm5

(-) Related Entries Specified in the PDB File

3eha CRYSTAL STRUCTURE OF DEATH ASSOCIATED PROTEIN KINASE COMPLEXED WITH AMPPNP
3lm5