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(-) Description

Title :  COMPLEX OF CK2 WITH A CDC7 INHIBITOR
 
Authors :  T. J. Stout
Date :  20 Mar 12  (Deposition) - 23 May 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Koltun, A. L. Tsuhako, D. S. Brown, N. Aay, A. Arcalas, V. Chan, H. Du, S. Engst, K. Ferguson, M. Franzini, A. Galan, C. R. Holst, P. Huang, B. Kane, M. H. Kim, J. Li, D. Markby, M. Mohan, K. Noson, A. Plonowski, S. J. Richards, S. Robertson, K. Shaw, G. Stott, T. J. Stout, J. Young, P. Yu, C. A. Zaharia, W. Zhang, P. Zhou, J. M. Nuss, W. Xu, P. C. Kearney
Discovery Of Xl413, A Potent And Selective Cdc7 Inhibitor.
Bioorg. Med. Chem. Lett. V. 22 3727 2012
PubMed-ID: 22560567  |  Reference-DOI: 10.1016/J.BMCL.2012.04.024

(-) 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
    Fragment: KINASE DOMAIN, RESIDUES 2-332
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CK II, CK2-ALPHA, CK2

 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
1WUL1Ligand/Ion8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:47 , VAL A:53 , ILE A:66 , LYS A:68 , VAL A:116 , HIS A:160 , ASN A:161 , ILE A:174 , ASP A:175 , HOH A:2223 , HOH A:2231 , HOH A:2356BINDING SITE FOR RESIDUE WUL A1334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ANM)

(-) 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 4ANM)

(-) 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 4ANM)

(-) 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:328
 aligned with CSK2A_MAIZE | P28523 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        
          CSK2A_MAIZE     1 MSKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLCGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNVYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENS 328
               SCOP domains d4anma_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.....hhh.eeeeeeeeee..eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.......eeeeee......eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4anm A   6 SSKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLCGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNVYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENS 333
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
   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 4ANM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ANM)

(-) 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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  CSK2A_MAIZE | P28523
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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 3kxn 3pvg 3pwd 3pzh 4dgm 4dgn 4dgo 4rlk

(-) Related Entries Specified in the PDB File

1daw CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2(ALPHA-SUBUNIT) AND MG-AMPPNP
1day CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2(ALPHA-SUBUNIT) AND MG-GMPPNP
1ds5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEXWITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THETETRAMERIC PROTEIN KINASE CK2 HOLOENZYME.
1f0q CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASECK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOREMODIN
1j91 CRYSTAL STRUCTURE OF Z. MAYS CK2 KINASE ALPHA SUBUNIT INCOMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 4,5,6, 7-TETRABROMOBENZOTRIAZOLE
1jam CRYSTAL STRUCTURE OF APO-FORM OF Z. MAYS CK2 PROTEIN KINASEALPHA SUBUNIT
1lp4 CRYSTAL STRUCTURE OF A BINARY COMPLEX OF THE CATALYTICSUBUNIT OF PROTEIN KINASE CK2 WITH MG-AMPPNP
1lpu LOW TEMPERATURE CRYSTAL STRUCTURE OF THE APO-FORM OF THECATALYTIC SUBUNIT OF PROTEIN KINASE CK2 FROM ZEA MAYS
1lr4 ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE APO-FORM OF THECATALYTIC SUBUNIT OF PROTEIN KINASE CK2 FROM ZEA MAYS
1m2p CRYSTAL STRUCTURE OF 1,8-DI-HYDROXY-4-NITRO- ANTHRAQUINONE/CK2 KINASE COMPLEX
1m2q CRYSTAL STRUCTURE OF 1,8-DI-HYDROXY-4-NITRO-XANTEN- 9-ONE/CK2 KINASE COMPLEX
1m2r CRYSTAL STRUCTURE OF 5,8-DI-AMINO-1,4-DI-HYDROXY- ANTHRAQUINONE/CK2 KINASE COMPLEX
1om1 CRYSTAL STRUCTURE OF MAIZE CK2 ALPHA IN COMPLEX WITH IQA
1zoe CRYSTAL STRUCTURE OF PROTEIN KINASE CK2 IN COMPLEX WITH TBB-DERIVATIVES INHIBITORS
1zog CRYSTAL STRUCTURE OF PROTEIN KINASE CK2 IN COMPLEX WITH TBB-DERIVATIVES
1zoh CRYSTAL STRUCTURE OF PROTEIN KINASE CK2 IN COMPLEX WITH TBB-DERIVATIVES INHIBITORS