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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RIBOSOMAL PROTEIN S6 KINASE
 
Authors :  J. R. C. Muniz, J. M. Elkins, J. Wang, E. Ugochukwu, E. Salah, O. King, S. Picaud, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp
Date :  20 Jul 09  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp-Binding, Polymorphism, Metal-Binding, Human, Kinase, Ribosomal, Magnesium, Transferase, Serine/Threonine-Protein Kinase, Phosphoprotein, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. C. Muniz, J. M. Elkins, J. Wang, E. Ugochukwu, E. Salah, O. King, S. Picaud, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp
Crystal Structure Of The Human Ribosomal Protein S6 Kinase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE
    ChainsA, B
    EC Number2.7.11.1
    FragmentRESIDUES 413-719
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPKINASE C FROM 341-385 AND PKINASE FROM 418-675
    Synonym90 KDA RIBOSOMAL PROTEIN S6 KINASE 1, P90-RSK 1, PP90RSK1, P90S6K, RIBOSOMAL S6 KINASE 1, MAP KINASE-ACTIVATED PROTEIN KINASE 1A, S6K-ALPHA 1, RSK-1, MAPKAPK1A
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA3Ligand/IonSODIUM ION
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:467 , HIS B:469 , ILE B:472 , THR B:474BINDING SITE FOR RESIDUE NA B1710
2AC2SOFTWARETHR B:612 , PRO B:613 , PHE B:614 , ALA B:615 , THR B:701BINDING SITE FOR RESIDUE NA B1711
3AC3SOFTWAREGLY A:467 , HIS A:469 , ILE A:472 , THR A:474 , HOH A:2011 , HOH A:2012BINDING SITE FOR RESIDUE NA A1709
4AC4SOFTWARELEU B:502 , MET B:607 , SER B:687 , HIS B:688BINDING SITE FOR RESIDUE CL B1712
5AC5SOFTWARETHR B:627 , ARG B:628 , SER B:631 , GLN B:683 , HOH B:2062BINDING SITE FOR RESIDUE PEG B1713
6AC6SOFTWAREGLU B:496 , LEU B:497 , LEU B:498 , LYS B:537 , PRO B:538 , SER B:539 , MET B:698 , HOH B:2122BINDING SITE FOR RESIDUE PEG B1714

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:575 -B:575

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A1_HUMAN68-94
424-447
 
  2-
A:424-447
B:424-447
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A1_HUMAN183-195
531-543
 
  2-
A:531-543
B:531-543

(-) Exons   (0, 0)

(no "Exon" information available for 2WNT)

(-) 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:281
 aligned with KS6A1_HUMAN | Q15418 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:293
                                   425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705   
          KS6A1_HUMAN   416 DGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDKSKRDPSEEIEILLRYGQHPNIITLKDVYDDGKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPECLRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDTPEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDLQLVKGAMAATYSALNSS 708
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------   2wntA02            ------------------2wntA02 A:455-473,A:492-708 Transferase(Phosphotransferase) domain 1                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeeeee......eeeeeeee.---.hhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhh.......hhh.eee.....hhh.eee......................---------........hhhhhh.hhhhhhhh...........hhhhhhhhh..........hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnt A 416 DGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDK---DPSEEIEILLRYGQHPNIITLKDVYDDGKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPECLRICDFGFAKQLRAENGLLMTPCYT---------KRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDTPEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDLQLVKGAMAATYSALNSS 708
                                   425       435       445     | 455       465       475       485       495       505       515       525       535       545       555       565       575 |       - |     595       605       615       625       635       645       655       665       675       685       695       705   
                                                             451 455                                                                                                                       577       587                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with KS6A1_HUMAN | Q15418 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:295
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704     
          KS6A1_HUMAN   415 SDGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDKSKRDPSEEIEILLRYGQHPNIITLKDVYDDGKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPECLRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDTPEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDLQLVKGAMAATYSALNSSK 709
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------2wntB02             ------------------2wntB02 B:454-473,B:492-709 Transferase(Phosphotransferase) domain 1                                                                                                                                                       CATH domains
           Pfam domains (1) ---Pkinase-2wntB01 B:418-675                                                                                                                                                                                                                                         ---------------------------------- Pfam domains (1)
           Pfam domains (2) ---Pkinase-2wntB02 B:418-675                                                                                                                                                                                                                                         ---------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee......eeeeeee......eeeeeeee.....hhhhhhhhhhh........eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhh.hhhhhhhhh.......hhh.eee.....hhh.eee.....................----------........hhhhhh.hhhhhhhh...........hhhhhhhhh...............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnt B 415 SDGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDKSKRDPSEEIEILLRYGQHPNIITLKDVYDDGKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPECLRICDFGFAKQLRAENGLLMTPCY----------KRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDTPEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDLQLVKGAMAATYSALNSSK 709
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574 |       -  |    594       604       614       624       634       644       654       664       674       684       694       704     
                                                                                                                                                                                           576        587                                                                                                                          

   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  (0, 0)

(no "SCOP Domain" information available for 2WNT)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KS6A1_HUMAN | Q15418)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine 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:0072574    hepatocyte proliferation    The multiplication or reproduction of hepatocytes, resulting in the expansion of a cell population. Hepatocytes form the main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules.
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    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:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:2000491    positive regulation of hepatic stellate cell activation    Any process that activates or increases the frequency, rate or extent of hepatic stellate cell activation.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043620    regulation of DNA-templated transcription in response to stress    Modulation of the frequency, rate or extent of transcription from a DNA template as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0043555    regulation of translation in response to stress    Modulation of the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KS6A1_HUMAN | Q154182z7q 2z7r 2z7s 3rny 3tei 4h3p 4nif 5csf 5csi 5csj 5csn

(-) Related Entries Specified in the PDB File

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