Crystal structure of PDE6D in complex with the inhibitor rac-2
Biology and Chemistry Report
  •   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 O43250     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B
    GO ID   Ontology GO Term Definition
    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. 
    33124   Regulation of GTP Catabolic Process  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    43086   Negative Regulation of Catalytic Activity  Any Process That Stops or Reduces the Activity of an Enzyme. 
    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. 
    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. 
    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. 
    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