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Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule
Biology and Chemistry Report
4AU8
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text TRANSFERASE, CDK2, ALZHEIMER DISEASE

    Polymeric Molecules

    Chain A,B
    Description CYCLIN-DEPENDENT KINASE 5 
    Fragment RESIDUES 2-292 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 33623.0 
    Source Method genetically manipulated  
    Entity Name CELL DIVISION PROTEIN KINASE 5, SERINE/THREONINE-PROTEIN KINASE PSSALRE, TAU PROTEIN KINASE II CATALYTIC SUBUNIT, TPKII CATALYTIC SUBUNIT 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    IMD  IMIDAZOLE  C3 H5 N2   69.09  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    Z3R  4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide  C11 H8 N2 O2 S3   296.39  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B CDK5_HUMAN A1XKG3     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.7.11.22      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    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. 
    7399   Nervous System Development  The Process Whose Specific Outcome Is the Progression of Nervous Tissue Over Time From Its Formation to Its Mature State. 
    8219   Cell Death  Any Biological Process That Results in Permanent Cessation of All Vital Functions of a Cell. a Cell Should Be Considered Dead When Any One of the Following Molecular or Morphological Criteria Is Met: (1) the Cell Has Lost the Integrity of Its Plasma Membrane; (2) the Cell Including Its Nucleus Has Undergone Complete Fragmentation Into Discrete Bodies (frequently Referred to As "apoptotic Bodies"); And/or (3) Its Corpse (or Its Fragments) Have Been Engulfed by an Adjacent Cell in Vivo. 
    9790   Embryo Development  The Process Whose Specific Outcome Is the Progression of an Embryo From Its Formation Until the End of Its Embryonic Life Stage. the End of the Embryonic Stage Is Organism Specific. For Example For Mammals the Process Would Begin with Zygote Formation and End with Birth. For Insects the Process Would Begin At Zygote Formation and End with Larval Hatching. For Plant Zygotic Embryos This Would Be From Zygote Formation to the End of Seed Dormancy. For Plant Vegetative Embryos This Would Be From the Initial Determination of the Cell or Group of Cells to Form an Embryo Until the Point When the Embryo Becomes Independent of the Parent Plant. 
    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. 
    30182   Neuron Differentiation  The Process in Which a Relatively Unspecialized Cell Acquires Specialized Features of a Neuron. 
    31175   Neuron Projection Development  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). 
    43525   Positive Regulation of Neuron Apoptotic Process  Any Process That Activates or Increases the Frequency Rate or Extent of Cell Death of Neurons by Apoptotic Process. 
    48167   Regulation of Synaptic Plasticity  A Process That Modulates Synaptic Plasticity the Ability of Synapses to Change As Circumstances Require. They May Alter Function Such As Increasing or Decreasing Their Sensitivity or They May Increase or Decrease in Actual Numbers. 
    48511   Rhythmic Process  Any Process Pertinent to the Generation and Maintenance of Rhythms in the Physiology of an Organism. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    61001   Regulation of Dendritic Spine Morphogenesis  Any Process That Modulates the Rate Frequency or Extent of Dendritic Spine Morphogenesis the Process in Which the Anatomical Structures of a Dendritic Spine Are Generated and Organized. a Dendritic Spine Is a Protrusion From a Dendrite and a Specialized Subcellular Compartment Involved in Synaptic Transmission. 
    2000273   Positive Regulation of Receptor Activity  Any Process That Activates or Increases the Frequency Rate or Extent of Receptor Activity. 
    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. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    14069   Postsynaptic Density  The Postsynaptic Density Is a Region That Lies Adjacent to the Cytoplasmic Face of the Postsynaptic Membrane At Excitatory Synapse. It Forms a Disc That Consists of a Range of Proteins with Different Functions Some of Which Contact the Cytoplasmic Domains of Ion Channels in the Postsynaptic Membrane. the Proteins Making Up the Disc Include Receptors and Structural Proteins Linked to the Actin Cytoskeleton. They Also Include Signalling Machinery Such As Protein Kinases and Phosphatases. the Postsynaptic Density May Be Part of a Neuron or a Muscle Cell or a Glial Cell. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    30027   Lamellipodium  A Thin Sheetlike Process Extended by the Leading Edge of a Crawling Fibroblast; Contains a Dense Meshwork of Actin Filaments. 
    30054   Cell Junction  A Cellular Component That Forms a Specialized Region of Connection Between Two Cells or Between a Cell and the Extracellular Matrix. At a Cell Junction Anchoring Proteins Extend Through the Plasma Membrane to Link Cytoskeletal Proteins in One Cell to Cytoskeletal Proteins in Neighboring Cells or to Proteins in the Extracellular Matrix. 
    30424   Axon  The Long Process of a Neuron That Conducts Nerve Impulses Usually Away From the Cell Body to the Terminals and Varicosities Which Are Sites of Storage and Release of Neurotransmitter. 
    30425   Dendrite  A Neuron Projection That Has a Short Tapering Often Branched Morphology Receives and Integrates Signals From Other Neurons or From Sensory Stimuli and Conducts a Nerve Impulse Towards the Axon or the Cell Body. in Most Neurons the Impulse Is Conveyed From Dendrites to Axon Via the Cell Body But in Some Types of Unipolar Neuron the Impulse Does Not Travel Via the Cell Body. 
    30426   Growth Cone  The Migrating Motile Tip of a Growing Nerve Cell Axon or Dendrite. 
    31594   Neuromuscular Junction  The Junction Between the Axon of a Motor Neuron and a Muscle Fiber. in Response to the Arrival of Action Potentials the Presynaptic Button Releases Molecules of Neurotransmitters Into the Synaptic Cleft. These Diffuse Across the Cleft and Transmit the Signal to the Postsynaptic Membrane of the Muscle Fiber Leading to a Change in Post Synaptic Potential. 
    42995   Cell Projection  A Prolongation or Process Extending From a Cell E.g. a Flagellum or Axon. 
    43025   Neuronal Cell Body  The Portion of a Neuron That Includes the Nucleus But Excludes Cell Projections Such As Axons and Dendrites. 
    43204   Perikaryon  The Portion of the Cell Soma (cell Body) That Excludes the Nucleus. 
    45202   Synapse  The Junction Between a Nerve Fiber of One Neuron and Another Neuron or Muscle Fiber or Glial Cell; the Site of Interneuronal Communication. As the Nerve Fiber Approaches the Synapse It Enlarges Into a Specialized Structure the Presynaptic Nerve Ending Which Contains Mitochondria and Synaptic Vesicles. At the Tip of the Nerve Ending Is the Presynaptic Membrane; Facing It and Separated From It by a Minute Cleft (the Synaptic Cleft) Is a Specialized Area of Membrane On the Receiving Cell Known As the Postsynaptic Membrane. in Response to the Arrival of Nerve Impulses the Presynaptic Nerve Ending Secretes Molecules of Neurotransmitters Into the Synaptic Cleft. These Diffuse Across the Cleft and Transmit the Signal to the Postsynaptic Membrane. 
    45211   Postsynaptic Membrane  A Specialized Area of Membrane Facing the Presynaptic Membrane On the Tip of the Nerve Ending and Separated From It by a Minute Cleft (the Synaptic Cleft). Neurotransmitters Across the Synaptic Cleft and Transmit the Signal to the Postsynaptic Membrane. 
    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. 
    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). 
    5176   Erbb 2 Class Receptor Binding  Interacting Selectively and Non Covalently with the Protein Tyrosine Kinase Receptor Neu/erbb 2/her2. 
    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. 
    30549   Acetylcholine Receptor Activator Activity  Interacting (directly or Indirectly) with Acetylcholine Receptors Such That the Proportion of Receptors in the Active Form Is Increased. 
    43125   Erbb 3 Class Receptor Binding  Interacting Selectively and Non Covalently with the Protein Tyrosine Kinase Receptor Erbb 3/her3. 
    50321   Tau Protein Kinase Activity  Catalysis of the Reaction: ATP + Tau Protein = Adp + O Phospho Tau Protein. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Line Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name PFASTBACHTB


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7q36 1020     cyclin-dependent kinase 5 CDK5