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(-) Description

Title :  CRYSTAL STRUCTURE OF Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR (2-DYMETHYLAMMINO-4,5,6,7-TETRABROMOBENZOIMIDAZOL-1YL-ACETIC ACID (K66)
 
Authors :  E. Papinutto, C. Franchin, R. Battistutta
Date :  03 Dec 09  (Deposition) - 17 Nov 10  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase Ck2-Inhibitor Complex, Atp-Binding, Kinase, Nucleotide-Binding, Serine/Threonine-Protein Kinase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sarno, E. Papinutto, C. Franchin, J. Bain, M. Elliott, F. Meggio, Z. Kazimierczuk, A. Orzeszko, G. Zanotti, R. Battistutta, L. A. Pinna
Atp Site-Directed Inhibitors Of Protein Kinase Ck2: An Update.
Curr Top Med Chem V. 11 1340 2011
PubMed-ID: 21513497
(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
    Expression System Vector TypePLASMID
    FragmentALPHA SUBUNIT
    GeneACK2
    Organism CommonMAIZE
    Organism ScientificZEA MAYS
    Organism Taxid4577
    SynonymCK2-ALPHA, CK II

 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
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2K661Ligand/Ion[4,5,6,7-TETRABROMO-2-(DIMETHYLAMINO)-1H-BENZIMIDAZOL-1-YL]ACETIC ACID
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:47 , VAL A:53 , ILE A:66 , LYS A:68 , PHE A:113 , GLU A:114 , VAL A:116 , MET A:163 , ILE A:174 , ASP A:175 , HOH A:334BINDING SITE FOR RESIDUE K66 A 1
2AC2SOFTWAREARG A:191 , VAL A:192 , ALA A:193 , ARG A:195 , LYS A:198 , HOH A:522BINDING SITE FOR RESIDUE PEG A 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:230 -Pro A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CSK2A_MAIZE40-63  1A:45-68
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CSK2A_MAIZE147-159  1A:152-164

(-) Exons   (0, 0)

(no "Exon" information available for 3KXH)

(-) 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:327
 aligned with CSK2A_MAIZE | P28523 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:327
                                    11        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       311       321       
          CSK2A_MAIZE     2 SKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLCGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNVYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENS 328
               SCOP domains d3kxha_ A: Protein kinase CK2, alpha subunit                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------Pkinase-3kxhA01 A:39-324                                                                                                                                                                                                                                                                      --------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh.....hhh.eeeeeeeeee..eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.......eeeeee......eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxh A   7 SKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLcGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNVYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENS 333
                                    16        26        36        46        56        66        76        86  |     96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       
                                                                                                             89-CSO                                                                                                                                                                                                                                                

   Legend:   → Mismatch (orange background)
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  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 3KXH)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSK2A_MAIZE | P28523)
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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSK2A_MAIZE | P285231daw 1day 1ds5 1f0q 1j91 1jam 1lp4 1lpu 1lr4 1m2p 1m2q 1m2r 1om1 1zoe 1zog 1zoh 2oxd 2oxx 2oxy 2pvh 2pvj 2pvk 2pvl 2pvm 2pvn 2qc6 3be9 3fl5 3kxg 3kxm 3kxn 3pvg 3pwd 3pzh 4anm 4dgm 4dgn 4dgo 4rlk

(-) Related Entries Specified in the PDB File

1zoh CRYSTAL STRUCTURE OF PROTEIN KINASE CK2 IN COMPLEX WITH TBB -DERIVATIVES INHIBITORS
2oxx PROTEIN KINASE CK2 IN COMPLEX WITH TETRABROMOBENZOIMIDAZOLE K17, K22 AND K32 INHIBITORS
3kxg
3kxj
3kxm
3kxn