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Crystal structure of PDE6D in complex with the inhibitor rac-2
Biology and Chemistry Report
4JVB
  •   Structure Details   Hide

    Structure Keywords

    Keywords Protein binding/inhibitor
    Text Immunoglobulin-like beta-sandwich, GDI-like solubilizing factor, prenyl binding, Protein binding-inhibitor complex

    Polymeric Molecules

    Chain B
    Description Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17585.3 
    Source Method genetically manipulated  
    Entity Name GMP-PDE delta, Protein p17 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    1M0  1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole  C38 H32 N4 O   560.69  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    B PDE6D_HUMAN O43924     

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B
    GO ID   Ontology GO Term Definition
    6996   Organelle Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of an Organelle Within a Cell. an Organelle Is an Organized Structure of Distinctive Morphology and Function. Includes the Nucleus Mitochondria Plastids Vacuoles Vesicles Ribosomes and the Cytoskeleton. Excludes the Plasma Membrane. 
    7601   Visual Perception  The Series of Events Required For an Organism to Receive a Visual Stimulus Convert It to a Molecular Signal and Recognize and Characterize the Signal. Visual Stimuli Are Detected in the Form of Photons and Are Processed to Form an Image. 
    8152   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. 
    34260   Negative Regulation of Gtpase Activity  Any Process That Stops or Reduces the Rate of GTP Hydrolysis by a Gtpase. 
    50896   Response to Stimulus  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. the Process Begins with Detection of the Stimulus and Ends with a Change in State or Activity or the Cell or Organism. 
    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. 
    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. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    30659   Cytoplasmic Vesicle Membrane  The Lipid Bilayer Surrounding a Cytoplasmic Vesicle. 
    31410   Cytoplasmic Vesicle  A Vesicle Formed of Membrane or Protein Found in the Cytoplasm of a Cell. 
    42995   Cell Projection  A Prolongation or Process Extending From a Cell E.g. a Flagellum or Axon. 
    72372   Primary Cilium  A Cilium Found On Many Different Cell Types That Is Typically Present in a Single Copy Per Cell. a Primary Cilium May Have a Variable Array of Axonemal Microtubules and May or May Not Contain Molecular Motors. 
    4114   3' 5' Cyclic Nucleotide Phosphodiesterase Activity  Catalysis of the Reaction: Nucleoside 3' 5' Cyclic Phosphate + H2o = Nucleoside 5' Phosphate. 
    5095   Gtpase Inhibitor Activity  Stops Prevents or Reduces the Activity of Any Enzyme That Catalyzes the Hydrolysis of GTP to GDP and Orthophosphate. 
    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). 
    17137   Rab Gtpase Binding  Interacting Selectively and Non Covalently with Rab Protein Any Member of the Rab Subfamily of the Ras Superfamily of Monomeric Gtpases. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene pde6d, pded
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2q35-q36 5147     phosphodiesterase 6D, cGMP-specific, rod, delta PDE6D