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(-) Description

Title :  STRUCTURE OF A HUMAN CK2ALPHA PRIME, THE PARALOG ISOFORM OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 FROM HOMO SAPIENS
 
Authors :  N. Bischoff, B. Olsen, J. Raaf, M. Bretner, O. -G. Issinger, K. Niefind
Date :  15 Aug 10  (Deposition) - 19 Jan 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Eukaryptic Protein Kinase Fold, Phospho Transferase, Atp Binding, Phosphorylation, Cytoplasm And Nucleus, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Bischoff, B. Olsen, J. Raaf, M. Bretner, O. G. Issinger, K. Niefind
Structural Basis Of The Reduced Affinity Between The Protei Kinase Ck2 Subunits Ck2Alpha Prime And Ck2Beta
J. Mol. Biol. V. 407 1 2011
PubMed-ID: 21241709  |  Reference-DOI: 10.1016/J.JMB.2011.01.020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASEIN KINASE II SUBUNIT ALPHA'
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCK2A2, CSNK2A2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCK II ALPHA'

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
14B01Ligand/Ion3-(4,5,6,7-TETRABROMO-1H-BENZOTRIAZOL-1-YL)PROPAN-1-OL
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:54 , VAL A:67 , LYS A:69 , PHE A:114 , GLU A:115 , ILE A:117 , MET A:164 , ILE A:175 , ASP A:176 , HOH A:398BINDING SITE FOR RESIDUE 4B0 A 351
2AC2SOFTWAREARG A:156 , ASN A:190BINDING SITE FOR RESIDUE CL A 352

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040416E188ACSK22_HUMANPolymorphism55911801AE188A

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CSK22_HUMAN46-69  1A:46-69
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CSK22_HUMAN153-165  1A:153-165

(-) Exons   (0, 0)

(no "Exon" information available for 3OFM)

(-) 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:325
 aligned with CSK22_HUMAN | P19784 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:325
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
          CSK22_HUMAN     8 SRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQ 332
               SCOP domains d3ofma_ A: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------Pkinase-3ofmA01 A:40-325                                                                                                                                                                                                                                                                      ------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....ee...eeeeeeeee...eeeeeeee....eeeeeeee...hhhhhhhhhhhhhhh........eeeeee......eeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh......hhhhhh...hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofm A   8 SRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQ 332
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     

   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 3OFM)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSK22_HUMAN | P19784)
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:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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: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:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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: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:0071174    mitotic spindle checkpoint    A mitotic cell cycle checkpoint that originates from the spindle and delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and oriented, the completion of anaphase until chromosomes are attached to the spindle, or mitotic exit and cytokinesis when the spindle does not form.
    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:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031519    PcG protein complex    A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
    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
        CSK22_HUMAN | P197843e3b 3u87 5m4u 5m56

(-) Related Entries Specified in the PDB File

1jwh STRUCTURE OF THE HETEROTETRAMERIC CK2 HOLOENZYME
3bqc BEST RESOLVED STRUCTURE OF THE PARALOG ISOENZYME CK2ALPHA
3e3b CK2ALPHA PRIME STRUCTURE WITH A DIFFERENT INHIBITOR