Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 CALMODULIN-DEPENDENT PROTEIN KINASE 1D
 
Authors :  J. E. Debreczeni, P. Rellos, O. Fedorov, F. H. Niesen, C. Bhatia, L. Shre E. Salah, C. Smee, S. Colebrook, G. Berridge, O. Gileadi, G. Bunkoczi, E. Ugochukwu, A. C. W. Pike, F. Von Delft, S. Knapp, M. Sundstrom, J. We C. H. Arrowsmith, A. Edwards
Date :  19 Dec 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Transferase, Atp-Binding, Nuclear Protein, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Debreczeni, P. Rellos, O. Fedorov, F. H. Niesen, C. Bhatia, L. Shrestha, E. Salah, C. Smee, S. Colebrook, G. Berridge, O. Gileadi, G. Bunkoczi, E. Ugochukwu, A. C. W. Pike, F. Von Delft, S. Knapp, M. Sundstrom, J. Weigelt, C. H. Arrowsmith, A. Edwards
Crystal Structure Of Human Calmodulin-Dependent Protein Kinase 1D
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D
    ChainsA, C
    EC Number2.7.11.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-ROSETTA
    Expression System VectorPNIC28-BSA4
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-333
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALMODULIN-DEPENDENT PROTEIN KINASE 1D, CAM KINASE ID, CAM KINASE I DELTA, CAMKI-DELTA, CAM-KI DELTA, CAMKI DELTA, CAMK1D, CAMKI-LIKE PROTEIN KINASE, CKLIK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1QPP2Ligand/IonN-(5-METHYL-1H-PYRAZOL-3-YL)-2-PHENYLQUINAZOLIN-4-AMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:29 , GLN A:99 , LEU A:100 , VAL A:101 , TRP A:306 , ALA A:309 , HOH A:2009BINDING SITE FOR RESIDUE QPP A1314
2AC2SOFTWARELEU C:29 , GLN C:99 , LEU C:100 , VAL C:101 , TRP C:306 , ALA C:309 , HOH C:2010BINDING SITE FOR RESIDUE QPP C1314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JC6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:242 -Pro A:243
2Ser C:242 -Pro C:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040599I66MKCC1D_HUMANPolymorphism34194224A/CI66M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KCC1D_HUMAN29-57
 
  2A:29-57
C:29-57
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KCC1D_HUMAN140-152
 
  2A:140-152
C:140-152

(-) Exons   (0, 0)

(no "Exon" information available for 2JC6)

(-) 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:278
 aligned with KCC1D_HUMAN | Q8IU85 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:303
                                    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   
          KCC1D_HUMAN    11 SWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMISDFGLSKMEGKGDVMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNAT 313
               SCOP domains d2jc6a_ A: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2jc6A01 A:11-100 Phosphorylase Kinase; domain 1                                           2jc6A02 A:101-279 Transferase(Phosphotransferase) domain 1                                                                                                                         ---------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhheeeeeeeee....eeeeeee.....eeeeeeee...-----.hhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee.--------------------....hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhhhhhhhh........hhhhhh.hhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PROTEIN_KINASE_ATP           ----------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jc6 A  11 SWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKA-----SSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMIS--------------------PGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNAT 313
                                    20        30        40        50       | -   |    70        80        90       100       110       120       130       140       150       160   |     -         -    |  190       200       210       220       230       240       250       260       270       280       290       300       310   
                                                                          58    64                                                                                                 164                  185                                                                                                                                

Chain C from PDB  Type:PROTEIN  Length:277
 aligned with KCC1D_HUMAN | Q8IU85 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:303
                                    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   
          KCC1D_HUMAN    11 SWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMISDFGLSKMEGKGDVMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNAT 313
               SCOP domains d2jc6c_ C: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2jc6C01 C:11-100 Phosphorylase Kinase; domain 1                                           2jc6C02 C:101-279 Transferase(Phosphotransferase) domain 1                                                                                                                         ---------------------------------- CATH domains
           Pfam domains (1) ------------Pkinase-2jc6C01 C:23-279                                                                                                                                                                                                                                         ---------------------------------- Pfam domains (1)
           Pfam domains (2) ------------Pkinase-2jc6C02 C:23-279                                                                                                                                                                                                                                         ---------------------------------- Pfam domains (2)
         Sec.struct. author ..eee..hhhhheeeeeeeee....eeeeeee.....eeeeeeee...------hhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee.--------------------....hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.............hhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PROTEIN_KINASE_ATP           ----------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jc6 C  11 SWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKA------SIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMIS--------------------PGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNAT 313
                                    20        30        40        50       | -    |   70        80        90       100       110       120       130       140       150       160   |     -         -    |  190       200       210       220       230       240       250       260       270       280       290       300       310   
                                                                          58     65                                                                                                164                  185                                                                                                                                

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (KCC1D_HUMAN | Q8IU85)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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:0032793    positive regulation of CREB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0060267    positive regulation of respiratory burst    Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050773    regulation of dendrite development    Any process that modulates the frequency, rate or extent of dendrite development.
    GO:0071622    regulation of granulocyte chemotaxis    Any process that modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus.
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.

 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
    QPP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:242 - Pro A:243   [ RasMol ]  
    Ser C:242 - Pro C:243   [ 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
  2jc6
    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
  KCC1D_HUMAN | Q8IU85
    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
  KCC1D_HUMAN | Q8IU85
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2JC6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JC6)