Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE 2, BETA, CAMKK2 KINASE DOMAIN IN COMPLEX WITH STO-609
 
Authors :  S. Yoshikawa, M. Kukimoto-Niino, M. Shirouzu, A. Suzuki, S. Lee, Y. Min S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  31 Oct 08  (Deposition) - 03 Nov 09  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium/Calmodulin-Dependent Protein Kinase Kinase 2, Beta, Sto-609, Camkk2, E. C. 2. 7. 11. 17, Phosphorylation, Ampkk, Metabolism, Atp- Binding, Kinase, Calmodulin-Binding, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kukimoto-Niino, S. Yoshikawa, T. Takagi, N. Ohsawa, Y. Tomabechi, T. Terada, M. Shirouzu, A. Suzuki, S. Lee, T. Yamauchi, M. Okada-Iwabu M. Iwabu, T. Kadowaki, Y. Minokoshi, S. Yokoyama
Crystal Structure Of The Ca2+/Calmodulin-Dependent Protein Kinase Kinase In Complex With The Inhibitor Sto-609
J. Biol. Chem. V. 286 22570 2011
PubMed-ID: 21504895  |  Reference-DOI: 10.1074/JBC.M111.251710

(-) Compounds

Molecule 1 - CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE 2
    ChainsA
    EC Number2.7.11.17
    EngineeredYES
    Expression SystemCELL FREE PROTEIN SYNTHESIS
    Expression System PlasmidPX070406-05
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE BETA, CAM-KINASE KINASE BETA, CAM-KK BETA, CAMKK BETA

 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
16091Ligand/Ion7-OXO-7H-BENZIMIDAZO[2,1-A]BENZ[DE]ISOQUINOLINE-3-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:28 , ILE A:172 , ALA A:193 , LYS A:195 , PHE A:268 , GLU A:269 , LEU A:270 , VAL A:271 , ASN A:272 , GLY A:274 , LEU A:320 , ASP A:331BINDING SITE FOR RESIDUE 609 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZV2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:279 -Pro A:280
2Gln A:413 -Pro A:414

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040612A182TKKCC2_HUMANUnclassified  ---AA183T
2UniProtVAR_020533R363CKKCC2_HUMANPolymorphism1132780AR364C

  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.KKCC2_HUMAN171-194  1A:172-195
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KKCC2_HUMAN308-320  1A:309-321

(-) Exons   (0, 0)

(no "Exon" information available for 2ZV2)

(-) 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:256
 aligned with KKCC2_HUMAN | Q96RR4 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:289
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439         
          KKCC2_HUMAN   160 VQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR 448
               SCOP domains d2zv2a_ A: aut  omated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2zv2A01 A:161-  270 Phosphorylase Kinase                               ; domain 1                             2zv2A02 A:271-449 Transferase(Phosphotransferase) domain 1                                                                                                                          CATH domains
               Pfam domains -----Pkinase-2  zv2A01 A:166-447                                                                                                                                                                                                                                                               -- Pfam domains
         Sec.struct. author .ee..eeeeeeee.--..eeeeeee....eeeeeeeee..-------------------------------hhhhhhhhhhhh........eeeeee.....eeeeeee................hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.....hhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zv2 A 161 VQLNQYTLKDEIGK--YGVVKLAYNENDNTYYAMKVLSKK-------------------------------EQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR 449
                                   170   |  |180       190       200         -         -         - |     240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440         
                                       174  |                    200                             232                                                                                                                                                                                                                         
                                          177                                                                                                                                                                                                                                                                                

   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  (1, 1)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KKCC2_HUMAN | Q96RR4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine 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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    609  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:413 - Pro A:414   [ RasMol ]  
    Val A:279 - Pro A:280   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2zv2
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KKCC2_HUMAN | Q96RR4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.17
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KKCC2_HUMAN | Q96RR4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KKCC2_HUMAN | Q96RR45uy6 5uyj 5vt1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZV2)