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MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX
Biology and Chemistry Report
1BI8
  •   Structure Details   Hide

    Structure Keywords

    Keywords COMPLEX (KINASE/INHIBITOR)
    Text CYCLIN DEPENDENT KINASE, CYCLIN DEPENDENT KINASE INHIBITORY PROTEIN, CDK, INK4, CELL CYCLE, COMPLEX (KINASE-INHIBITOR), COMPLEX (KINASE-INHIBITOR) complex

    Polymeric Molecules

    Chain A,C
    Description CYCLIN-DEPENDENT KINASE 6 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 36987.7 
    Source Method genetically manipulated  
    Entity Name CDK6 
    Chain B,D
    Description CYCLIN-DEPENDENT KINASE INHIBITOR 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17723.3 
    Source Method genetically manipulated  
    Entity Name P19INK4D 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C CDK6_HUMAN Q00534     
    B,D CDN2D_HUMAN P55273     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A C  2.7.11.22        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    16310   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. 
    30154   Cell Differentiation  The Process in Which Relatively Unspecialized Cells E.g. Embryonic or Regenerative Cells Acquire Specialized Structural And/or Functional Features That Characterize the Cells Tissues or Organs of the Mature Organism or Some Other Relatively Stable Phase of the Organism's Life History. Differentiation Includes the Processes Involved in Commitment of a Cell to a Specific Fate and Its Subsequent Development to the Mature State. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    1726   Ruffle  Projection At the Leading Edge of a Crawling Cell; the Protrusions Are Supported by a Microfilament Meshwork. 
    5634   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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    42995   Cell Projection  A Prolongation or Process Extending From a Cell E.g. a Flagellum or Axon. 
    166   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. 
    4674   Protein Serine/threonine Kinase Activity  Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   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. 
    30332   Cyclin Binding  Interacting Selectively and Non Covalently with Cyclins Proteins Whose Levels in a Cell Varies Markedly During the Cell Cycle Rising Steadily Until Mitosis Then Falling Abruptly to Zero. As Cyclins Reach a Threshold Level They Are Thought to Drive Cells Into G2 Phase and Thus to Mitosis. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    5634   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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    19901   Protein Kinase Binding  Interacting Selectively and Non Covalently with a Protein Kinase Any Enzyme That Catalyzes the Transfer of a Phosphate Group Usually From ATP to a Protein Substrate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Cell Line Spodoptera Frugiperda
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Hi5
    Host Vector Glutathione S Transferase Fusion


    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Cell Line Spodoptera Frugiperda
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Genus Spodoptera
    Host Strain Hi5
    Host Vector Baculovirus


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7q21-q22 1021     cyclin-dependent kinase 6 CDK6    
    19 19p13 1032     cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) CDKN2D    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs200082521 LS-SNP   dbSNP   A 86 S - > P Beta Ladder 35% (Intermediate) 7 92404123
    rs35654944 LS-SNP   dbSNP   A 110 D - > N Turn 62% (Exposed) 7 92404051
    rs150037621 LS-SNP   dbSNP   B 67 P - > L Bend 18% (Intermediate) 19 10678035
    rs188751101 LS-SNP   dbSNP   B 88 D - > H Helix 36% (Exposed) 19 10677973
    rs150872881 LS-SNP   dbSNP   B 94 V - > M Helix 15% (Intermediate) 19 10677955
    rs141595298 LS-SNP   dbSNP   B 102 V - > M Coil 15% (Intermediate) 19 10677931
    rs183848909 LS-SNP   dbSNP   B 103 P - > S Coil 32% (Intermediate) 19 10677928
    rs139314642 LS-SNP   dbSNP   B 121 A - > S Helix 54% (Exposed) 19 10677874
    rs200543818 LS-SNP   dbSNP   B 142 P - > S Helix 0% (Buried) 19 10677811