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(-) Description

Title :  STRUCTURE OF CASEIN KINASE GAMMA 3 IN COMPLEX WITH INHIBITOR
 
Authors :  G. Bunkoczi, E. Salah, P. Rellos, S. Das, O. Fedorov, P. Savitsky, J. E. Debreczeni, O. Gileadi, M. Sundstrom, A. Edwards, C. Arrowsmith J. Weigelt, F. Von Delft, S. Knapp
Date :  26 Jul 06  (Deposition) - 01 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine/Threonine-Protein Kinase, Kinase, Transferase, Atp- Binding, Phosphorylation, Nucleotide-Binding, Wnt Signaling Pathway, Serine/Threonine Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Bunkoczi, E. Salah, P. Rellos, S. Das, O. Fedorov, P. Savitsky, J. E. Debreczeni, O. Gileadi, M. Sundstrom, A. Edwards, C. Arrowsmith J. Weigelt, F. Von Delft, S. Knapp
Inhibitor Binding By Casein Kinases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CASEIN KINASE I ISOFORM GAMMA-3
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineDE3
    Expression System PlasmidPLIC-SGC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 35-362
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCKI-GAMMA 3, CASEIN KINASE 1 GAMMA 3

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL
2P011Ligand/Ion2-({6-[(3-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:214 , GLN A:250 , GLY A:251 , ARG A:260 , HOH A:2360 , HOH A:2361BINDING SITE FOR RESIDUE PO4 A1337
2AC2SOFTWAREILE A:49 , LEU A:57 , ALA A:70 , GLU A:117 , LEU A:119 , GLY A:120 , GLU A:166 , LEU A:169 , ILE A:184 , PRO A:331 , THR A:332 , PRO A:333 , HOH A:2124 , HOH A:2359BINDING SITE FOR RESIDUE P01 A1335
3AC3SOFTWARETYR A:289 , ASP A:300 , TYR A:303 , HOH A:2298BINDING SITE FOR RESIDUE EDO A1336

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IZU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KC1G3_HUMAN49-72  1A:49-72
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KC1G3_HUMAN158-170  1A:158-170

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000003619912dENSE00000998779chr5:122881328-122881535208KC1G3_HUMAN1-60601A:36-60 (gaps)25
1.3bENST000003619913bENSE00001121014chr5:122888801-12288884141KC1G3_HUMAN60-73141A:60-7314
1.4ENST000003619914ENSE00000998771chr5:122893189-12289325870KC1G3_HUMAN74-97241A:74-9724
1.5bENST000003619915bENSE00001120994chr5:122909087-122909235149KC1G3_HUMAN97-146501A:97-14650
1.6ENST000003619916ENSE00000998778chr5:122911423-122911657235KC1G3_HUMAN147-225791A:147-22579
1.7ENST000003619917ENSE00001736478chr5:122923762-12292384786KC1G3_HUMAN225-253291A:225-25329
1.8bENST000003619918bENSE00000998775chr5:122924121-12292420585KC1G3_HUMAN254-282291A:254-28229
1.9bENST000003619919bENSE00001082724chr5:122926107-122926252146KC1G3_HUMAN282-330491A:282-33049
1.10ENST0000036199110ENSE00001120965chr5:122927013-12292710896KC1G3_HUMAN331-362321A:331-3344
1.11ENST0000036199111ENSE00001082720chr5:122930733-12293082896KC1G3_HUMAN363-394320--
1.12ENST0000036199112ENSE00000998768chr5:122940418-122940524107KC1G3_HUMAN395-430360--
1.14eENST0000036199114eENSE00001431703chr5:122950036-1229511401105KC1G3_HUMAN430-447180--

(-) 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:297
 aligned with KC1G3_HUMAN | Q9Y6M4 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:299
                                    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         
          KC1G3_HUMAN    36 VLMVGPNFRVGKKIGCGNFGELRLGKNLYTNEYVAIKLEPMKSRAPQLHLEYRFYKQLGSGDGIPQVYYFGPCGKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKTQQVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRATPIEVLCENFPEMATYLRYVRRLDFFEKPDYDYLRKLFTDLFDRKGYMFDYEYDWIGKQLPTPV 334
               SCOP domains d2izua_ A: autom  ated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2izuA01 A:36-119   Phosphorylase Kinase; domain 1                                   2izuA02 A:120-334 Transferase(Phosphotransferase) domain 1                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeeeeeee.--..eeeeeee....eeeeeeeee......hhhhhhhhhhhhh.......eeeeeee..eeeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.ee............ee......ee.........................hhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d UniProt: 1-60  -------------Exon 1.4  PDB: A:74-97  -------------------------------------------------Exon 1.6  PDB: A:147-225 UniProt: 147-225                                      ----------------------------Exon 1.8b  PDB: A:254-282    ------------------------------------------------1.10 Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.3b     -----------------------Exon 1.5b  PDB: A:97-146 UniProt: 97-146          ------------------------------------------------------------------------------Exon 1.7  PDB: A:225-253     ----------------------------Exon 1.9b  PDB: A:282-330 UniProt: 282-330       ---- Transcript 1 (2)
                 2izu A  36 VLMVGPNFRVGKKIGC--FGELRLGKNLYTNEYVAIKLEPMKSRAPQLHLEYRFYKQLGSGDGIPQVYYFGPCGKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKTQQVIHIIDFALAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRATPIEVLCENFPEMATYLRYVRRLDFFEKPDYDYLRKLFTDLFDRKGYMFDYEYDWIGKQLPTPV 334
                                    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         
                                          51 54                                                                                                                                                                                                                                                                                        

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IZU)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KC1G3_HUMAN | Q9Y6M4)
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: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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    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: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
        KC1G3_HUMAN | Q9Y6M42chl 2izr 2izs 2izt 4g16 4g17 4hgl 4hgs

(-) Related Entries Specified in the PDB File

2chl STRUCTURE OF CASEIN KINASE 1 GAMMA 3
2iur CRYSTAL STRUCTURE OF N-QUINOL FORM OF AROMATIC AMINE DEHYDROGENASE (AADH) FROM ALCALIGENES FAECALIS, FORM A COCRYSTAL COMPLEX WITH INHIBITOR
2izs STRUCTURE OF CASEIN KINASE GAMMA 3 IN COMPLEX WITH INHIBITOR
2izt STRUCTURE OF CASEIN KINASE GAMMA 3 IN COMPLEX WITH INHIBITOR