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(-) Description

Title :  CRYSTAL STRUCTURE OF Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR TETRAIODOBENZIMIDAZOLE (K88)
 
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 :  2.00
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
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALPHA SUBUNIT
    Gene: ACK2
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CK2-ALPHA, CK II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1K8X1Ligand/Ion4,5,6,7-TETRAIODO-1H-BENZIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:45 , GLY A:46 , VAL A:53 , ILE A:66 , PHE A:113 , GLU A:114 , VAL A:116 , MET A:163 , ILE A:174 , HOH A:480BINDING SITE FOR RESIDUE K8X A 1

(-) SS Bonds  (0, 0)

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

(-) 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 3KXN)

(-) 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 3KXN)

(-) 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 d3kxna_ A: Protein kinase CK2, alpha subunit                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------Pkinase-3kxnA01 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........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxn 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
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) 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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  3kxn
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CSK2A_MAIZE | P28523: 1daw 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 3kxh 3kxm 3pvg 3pwd 3pzh 4anm 4dgm 4dgn 4dgo 4rlk

(-) Related Entries Specified in the PDB File

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2oxx PROTEIN KINASE CK2 IN COMPLEX WITH TETRABROMOBENZOIMIDAZOLE K17, K22 AND K32 INHIBITORS
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