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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 A4D1G0     
    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
    82   G1/s Transition of Mitotic Cell Cycle  The Mitotic Cell Cycle Transition by Which a Cell in G1 Commits to S Phase. the Process Begins with the Build Up of G1 Cyclin Dependent Kinase (g1 Cdk) Resulting in the Activation of Transcription of G1 Cyclins. the Process Ends with the Positive Feedback of the G1 Cyclins On the G1 Cdk Which Commits the Cell to S Phase in Which DNA Replication Is Initiated. 
    278   Mitotic Cell Cycle  Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 
    1954   Positive Regulation of Cell Matrix Adhesion  Any Process That Activates or Increases the Rate or Extent of Cell Adhesion to an Extracellular Matrix. 
    2244   Hematopoietic Progenitor Cell Differentiation  The Process in Which Precursor Cell Type Acquires the Specialized Features of a Hematopoietic Progenitor Cell a Class of Cell Types Including Myeloid Progenitor Cells and Lymphoid Progenitor Cells. 
    3323   Type B Pancreatic Cell Development  The Process Whose Specific Outcome Is the Progression of a Type B Pancreatic Cell Over Time From Its Formation to the Mature Structure. a Type B Pancreatic Cell Is a Cell Located Towards Center of the Islets of Langerhans That Secretes Insulin. 
    6468   Protein Phosphorylation  The Process of Introducing a Phosphate Group On to a Protein. 
    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. 
    7050   Cell Cycle Arrest  A Regulatory Process That Halts Progression Through the Cell Cycle During One of the Normal Phases (g1 S G2 M). 
    7219   Notch Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of an Extracellular Ligand to the Receptor Notch On the Surface of a Target Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    8285   Negative Regulation of Cell Proliferation  Any Process That Stops Prevents or Reduces the Rate or Extent of Cell Proliferation. 
    9615   Response to Virus  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus From a Virus. 
    10468   Regulation of Gene Expression  Any Process That Modulates the Frequency Rate or Extent of Gene Expression. Gene Expression Is the Process in Which a Gene's Coding Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    10628   Positive Regulation of Gene Expression  Any Process That Increases the Frequency Rate or Extent of Gene Expression. Gene Expression Is the Process in Which a Gene's Coding Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    14002   Astrocyte Development  The Process Aimed At the Progression of an Astrocyte Over Time From Initial Commitment of the Cell to a Specific Fate to the Fully Functional Differentiated Cell. an Astrocyte Is the Most Abundant Type of Glial Cell. Astrocytes Provide Support For Neurons and Regulate the Environment in Which They Function. 
    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. 
    21542   Dentate Gyrus Development  The Process Whose Specific Outcome Is the Progression of the Dentate Gyrus Over Time From Its Formation to the Mature Structure. the Dentate Gyrus Is One of Two Interlocking Gyri of the Hippocampus. It Contains Granule Cells Which Project to the Pyramidal Cells and Interneurons of the Ca3 Region of the Ammon Gyrus. 
    21670   Lateral Ventricle Development  The Process Whose Specific Outcome Is the Progression of the Lateral Ventricles Over Time From the Formation to the Mature Structure. the Two Lateral Ventricles Are a Cavity in Each of the Cerebral Hemispheres Derived From the Cavity of the Embryonic Neural Tube. They Are Separated From Each Other by the Septum Pellucidum and Each Communicates with the Third Ventricle by the Foramen of Monro Through Which Also the Choroid Plexuses of the Lateral Ventricles Become Continuous with That of the Third Ventricle. 
    30097   Hemopoiesis  The Process Whose Specific Outcome Is the Progression of the Myeloid and Lymphoid Derived Organ/tissue Systems of the Blood and Other Parts of the Body Over Time From Formation to the Mature Structure. the Site of Hemopoiesis Is Variable During Development But Occurs Primarily in Bone Marrow or Kidney in Many Adult Vertebrates. 
    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. 
    33077   T Cell Differentiation in Thymus  The Process in Which a Precursor Cell Type Acquires the Specialized Features of a T Cell Via a Differentiation Pathway Dependent Upon Transit Through the Thymus. 
    42063   Gliogenesis  The Process That Results in the Generation of Glial Cells. This Includes the Production of Glial Progenitors and Their Differentiation Into Mature Glia. 
    42127   Regulation of Cell Proliferation  Any Process That Modulates the Frequency Rate or Extent of Cell Proliferation. 
    43697   Cell Dedifferentiation  The Process in Which a Specialized Cell Loses the Structural or Functional Features That Characterize It in the Mature Organism or Some Other Relatively Stable Phase of the Organism's Life History. Under Certain Conditions These Cells Can Revert Back to the Features of the Stem Cells That Were Their Ancestors. 
    45596   Negative Regulation of Cell Differentiation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Differentiation. 
    45638   Negative Regulation of Myeloid Cell Differentiation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Myeloid Cell Differentiation. 
    45646   Regulation of Erythrocyte Differentiation  Any Process That Modulates the Frequency Rate or Extent of Erythrocyte Differentiation. 
    45668   Negative Regulation of Osteoblast Differentiation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Osteoblast Differentiation. 
    45786   Negative Regulation of Cell Cycle  Any Process That Stops Prevents or Reduces the Rate or Extent of Progression Through the Cell Cycle. 
    48146   Positive Regulation of Fibroblast Proliferation  Any Process That Activates or Increases the Frequency Rate or Extent of Multiplication or Reproduction of Fibroblast Cells. 
    48699   Generation of Neurons  The Process in Which Nerve Cells Are Generated. This Includes the Production of Neuroblasts and Their Differentiation Into Neurons. 
    50680   Negative Regulation of Epithelial Cell Proliferation  Any Process That Stops Prevents or Reduces the Rate or Extent of Epithelial Cell Proliferation. 
    51301   Cell Division  The Process Resulting in Division and Partitioning of Components of a Cell to Form More Cells; May or May Not Be Accompanied by the Physical Separation of a Cell Into Distinct Individually Membrane Bounded Daughter Cells. 
    60218   Hematopoietic Stem Cell Differentiation  The Process in Which a Relatively Unspecialized Cell Acquires Specialized Features of a Hematopoietic Stem Cell. a Stem Cell Is a Cell That Retains the Ability to Divide and Proliferate Throughout Life to Provide Progenitor Cells That Can Differentiate Into Specialized Cells. 
    2000145   Regulation of Cell Motility  Any Process That Modulates the Frequency Rate or Extent of Cell Motility. 
    2000773   Negative Regulation of Cellular Senescence  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cellular Senescence. 
    307   Cyclin Dependent Protein Kinase Holoenzyme Complex  Cyclin Dependent Protein Kinases (cdks) Are Enzyme Complexes That Contain a Kinase Catalytic Subunit Associated with a Regulatory Cyclin Partner. 
    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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5813   Centrosome  A Structure Comprised of a Core Structure (in Most Organisms a Pair of Centrioles) and Peripheral Material From Which a Microtubule Based Structure Such As a Spindle Apparatus Is Organized. Centrosomes Occur Close to the Nucleus During Interphase in Many Eukaryotic Cells Though in Animal Cells It Changes Continually During the Cell Division Cycle. 
    5815   Microtubule Organizing Center  An Intracellular Structure That Can Catalyze Gamma Tubulin Dependent Microtubule Nucleation and That Can Anchor Microtubules by Interacting with Their Minus Ends Plus Ends or Sides. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5856   Cytoskeleton  Any of the Various Filamentous Elements That Form the Internal Framework of Cells and Typically Remain After Treatment of the Cells with Mild Detergent to Remove Membrane Constituents and Soluble Components of the Cytoplasm. the Term Embraces Intermediate Filaments Microfilaments Microtubules the Microtrabecular Lattice and Other Structures Characterized by a Polymeric Filamentous Nature and Long Range Order Within the Cell. the Various Elements of the Cytoskeleton Not Only Serve in the Maintenance of Cellular Shape But Also Have Roles in Other Cellular Functions Including Cellular Movement Cell Division Endocytosis and Movement of Organelles. 
    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. 
    4672   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. 
    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. 
    4693   Cyclin Dependent Protein Serine/threonine Kinase Activity  Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. This Reaction Requires the Binding of a Regulatory Cyclin Subunit and Full Activity Requires Stimulatory Phosphorylation by a Cdk Activating Kinase (cak). 
    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. 
    16772   Transferase Activity Transferring Phosphorus Containing Groups  Catalysis of the Transfer of a Phosphorus Containing Group From One Compound (donor) to Another (acceptor). 
    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
    79   Regulation of Cyclin Dependent Protein Serine/threonine Kinase Activity  Any Process That Modulates the Frequency Rate or Extent of Cyclin Dependent Protein Serine/threonine Kinase Activity. 
    82   G1/s Transition of Mitotic Cell Cycle  The Mitotic Cell Cycle Transition by Which a Cell in G1 Commits to S Phase. the Process Begins with the Build Up of G1 Cyclin Dependent Kinase (g1 Cdk) Resulting in the Activation of Transcription of G1 Cyclins. the Process Ends with the Positive Feedback of the G1 Cyclins On the G1 Cdk Which Commits the Cell to S Phase in Which DNA Replication Is Initiated. 
    278   Mitotic Cell Cycle  Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 
    731   DNA Synthesis Involved in DNA Repair  Synthesis of DNA That Proceeds From the Broken 3' Single Strand DNA End Uses the Homologous Intact Duplex As the Template. 
    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. 
    7050   Cell Cycle Arrest  A Regulatory Process That Halts Progression Through the Cell Cycle During One of the Normal Phases (g1 S G2 M). 
    7605   Sensory Perception of Sound  The Series of Events Required For an Organism to Receive an Auditory Stimulus Convert It to a Molecular Signal and Recognize and Characterize the Signal. Sonic Stimuli Are Detected in the Form of Vibrations and Are Processed to Form a Sound. 
    8285   Negative Regulation of Cell Proliferation  Any Process That Stops Prevents or Reduces the Rate or Extent of Cell Proliferation. 
    9411   Response to Uv  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Ultraviolet Radiation (uv Light) Stimulus. Ultraviolet Radiation Is Electromagnetic Radiation with a Wavelength in the Range of 10 to 380 Nanometers. 
    30308   Negative Regulation of Cell Growth  Any Process That Stops Prevents or Reduces the Frequency Rate Extent or Direction of Cell Growth. 
    32526   Response to Retinoic Acid  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Retinoic Acid Stimulus. 
    33280   Response to Vitamin D  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Vitamin D Stimulus. 
    42326   Negative Regulation of Phosphorylation  Any Process That Stops Prevents or Decreases the Rate of Addition of Phosphate Groups to a Molecule. 
    43154   Negative Regulation of Cysteine Type Endopeptidase Activity Involved in Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of a Cysteine Type Endopeptidase Activity Involved in the Apoptotic Process. 
    48102   Autophagic Cell Death  A Form of Programmed Cell Death That Is Accompanied by Macroautophagy Which Is Characterized by the Sequestration of Cytoplasmic Material Within Autophagosomes For Bulk Degradation by Lysosomes. Autophagic Cell Death Is Characterized by Lack of Chromatin Condensation Massive Vacuolization of the Cytoplasm and Accumulation of (double Membraned) Autophagic Vacuoles with Little or No Uptake by Phagocytic Cells. 
    71901   Negative Regulation of Protein Serine/threonine Kinase Activity  Any Process That Decreases the Rate Frequency or Extent of Protein Serine/threonine Kinase Activity. 
    1902230   Negative Regulation of Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage. 
    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. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    4861   Cyclin Dependent Protein Serine/threonine Kinase Inhibitor Activity  Stops Prevents or Reduces the Activity of a Cyclin Dependent Protein Serine/threonine Kinase. 
    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