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Crystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum Retinol-binding Protein at 2.0 A Resolution
Biology and Chemistry Report
1JYJ
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSPORT PROTEIN
    Text retinol binding protein, lipocalin family, beta barrel, TRANSPORT PROTEIN

    Polymeric Molecules

    Chain A
    Description PLASMA RETINOL-BINDING PROTEIN 
    Mutation W67L, W91H 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 20994.7 
    Source Method genetically manipulated  
    Entity Name PRBP 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A RET4_HUMAN P02753     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    1523   Retinoid Metabolic Process  The Chemical Reactions and Pathways Involving Retinoids Any Member of a Class of Isoprenoids That Contain or Are Derived From Four Prenyl Groups Linked Head to Tail. Retinoids Include Retinol and Retinal and Structurally Similar Natural Derivatives or Synthetic Compounds But Need Not Have Vitamin a Activity. 
    1654   Eye Development  The Process Whose Specific Outcome Is the Progression of the Eye Over Time From Its Formation to the Mature Structure. the Eye Is the Organ of Sight. 
    6094   Gluconeogenesis  The Formation of Glucose From Noncarbohydrate Precursors Such As Pyruvate Amino Acids and Glycerol. 
    6810   Transport  The Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells or Within a Multicellular Organism by Means of Some Agent Such As a Transporter or Pore. 
    7283   Spermatogenesis  The Process of Formation of Spermatozoa Including Spermatocytogenesis and Spermiogenesis. 
    7507   Heart Development  The Process Whose Specific Outcome Is the Progression of the Heart Over Time From Its Formation to the Mature Structure. the Heart Is a Hollow Muscular Organ Which by Contracting Rhythmically Keeps Up the Circulation of the Blood. 
    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. 
    7603   Phototransduction Visible Light  The Sequence of Reactions Within a Cell Required to Convert Absorbed Photons From Visible Light Into a Molecular Signal. a Visible Light Stimulus Is Electromagnetic Radiation That Can Be Perceived Visually by an Organism; For Organisms Lacking a Visual System This Can Be Defined As Light with a Wavelength Within the Range 380 to 780 Nm. 
    8584   Male Gonad Development  The Process Whose Specific Outcome Is the Progression of the Male Gonad Over Time From Its Formation to the Mature Structure. 
    30277   Maintenance of Gastrointestinal Epithelium  Protection of Epithelial Surfaces of the Gastrointestinal Tract From Proteolytic and Caustic Digestive Agents. 
    30324   Lung Development  The Process Whose Specific Outcome Is the Progression of the Lung Over Time From Its Formation to the Mature Structure. in All Air Breathing Vertebrates the Lungs Are Developed From the Ventral Wall of the Oesophagus As a Pouch Which Divides Into Two Sacs. in Amphibians and Many Reptiles the Lungs Retain Very Nearly This Primitive Sac Like Character But in the Higher Forms the Connection with the Esophagus Becomes Elongated Into the Windpipe and the Inner Walls of the Sacs Become More and More Divided Until in the Mammals the Air Spaces Become Minutely Divided Into Tubes Ending in Small Air Cells in the Walls of Which the Blood Circulates in a Fine Network of Capillaries. in Mammals the Lungs Are More or Less Divided Into Lobes and Each Lung Occupies a Separate Cavity in the Thorax. 
    32024   Positive Regulation of Insulin Secretion  Any Process That Activates or Increases the Frequency Rate or Extent of the Regulated Release of Insulin. 
    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. 
    32868   Response to Insulin  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 Insulin Stimulus. Insulin Is a Polypeptide Hormone Produced by the Islets of Langerhans of the Pancreas in Mammals and by the Homologous Organs of Other Organisms. 
    34633   Retinol Transport  The Directed Movement of Retinol Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. Retinol Is Vitamin A1 2 6 6 Trimethyl 1 (9' Hydroxy 3' 7' Dimethylnona 1' 3' 5' 7' Tetraenyl)cyclohex 1 Ene One of the Three Components That Makes Up Vitamin A. 
    42572   Retinol Metabolic Process  The Chemical Reactions and Pathways Involving Retinol One of the Three Compounds That Makes Up Vitamin A. 
    42574   Retinal Metabolic Process  The Chemical Reactions and Pathways Involving Retinal a Compound That Plays an Important Role in the Visual Process in Most Vertebrates. in the Retina Retinal Combines with Opsins to Form Visual Pigments. Retinal Is One of the Forms of Vitamin A. 
    42593   Glucose Homeostasis  Any Process Involved in the Maintenance of an Internal Steady State of Glucose Within an Organism or Cell. 
    45471   Response to Ethanol  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 Ethanol Stimulus. 
    48562   Embryonic Organ Morphogenesis  Morphogenesis During the Embryonic Phase of a Tissue or Tissues That Work Together to Perform a Specific Function or Functions. Morphogenesis Is the Process in Which Anatomical Structures Are Generated and Organized. Organs Are Commonly Observed As Visibly Distinct Structures But May Also Exist As Loosely Associated Clusters of Cells That Work Together to Perform a Specific Function or Functions. 
    48706   Embryonic Skeletal System Development  The Process Occurring During the Embryonic Phase Whose Specific Outcome Is the Progression of the Skeleton Over Time From Its Formation to the Mature Structure. 
    48738   Cardiac Muscle Tissue Development  The Process Whose Specific Outcome Is the Progression of Cardiac Muscle Over Time From Its Formation to the Mature Structure. 
    48807   Female Genitalia Morphogenesis  The Process in Which the Anatomical Structures of Female Genitalia Are Generated and Organized. 
    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. 
    50908   Detection of Light Stimulus Involved in Visual Perception  The Series of Events Involved in Visual Perception in Which a Light Stimulus Is Received and Converted Into a Molecular Signal. 
    51024   Positive Regulation of Immunoglobulin Secretion  Any Process That Activates or Increases the Frequency Rate or Extent of the Regulated Release of Immunoglobulins From a Cell. 
    60041   Retina Development in Camera Type Eye  The Process Whose Specific Outcome Is the Progression of the Retina Over Time From Its Formation to the Mature Structure. the Retina Is the Innermost Layer or Coating At the Back of the Eyeball Which Is Sensitive to Light and in Which the Optic Nerve Terminates. 
    60044   Negative Regulation of Cardiac Muscle Cell Proliferation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cardiac Muscle Cell Proliferation. 
    60059   Embryonic Retina Morphogenesis in Camera Type Eye  The Process in Which the Anatomical Structure of the Retina Is Generated and Organized in a Camera Type Eye During the Embryonic Life Stage. 
    60065   Uterus Development  The Reproductive Developmental Process Whose Specific Outcome Is the Progression of the Uterus Over Time From Its Formation to the Mature Structure. 
    60068   Vagina Development  The Reproductive Developmental Process Whose Specific Outcome Is the Progression of the Vagina Over Time From Its Formation to the Mature Structure. 
    60157   Urinary Bladder Development  The Process Whose Specific Outcome Is the Progression of the Urinary Bladder Over Time From Its Formation to the Mature Structure. the Urinary Bladder Is an Elastic Muscular Sac Situated in the Anterior Part of the Pelvic Cavity in Which Urine Collects Before Excretion. 
    60347   Heart Trabecula Formation  The Process of Creating a Trabecula in the Heart. a Trabecula Is a Tissue Element in the Form of a Small Beam Strut or Rod. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    5215   Transporter Activity  Enables the Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells. 
    5501   Retinoid Binding  Interacting Selectively and Non Covalently with Retinoids Any Member of a Class of Isoprenoids That Contain or Are Derived From Four Prenyl Groups Linked Head to Tail. Retinoids Include Retinol and Retinal and Structurally Similar Natural Derivatives or Synthetic Compounds But Need Not Have Vitamin a Activity. 
    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). 
    16918   Retinal Binding  Interacting Selectively and Non Covalently with Retinal One of the Forms of Vitamin A. Retinal Plays an Important Role in the Visual Process in Most Vertebrates Combining with Opsins to Form Visual Pigments in the Retina. 
    19841   Retinol Binding  Interacting Selectively and Non Covalently with Retinol Vitamin A1 2 6 6 Trimethyl 1 (9' Hydroxy 3' 7' Dimethylnona 1' 3' 5' 7' Tetraenyl)cyclohex 1 Ene One of the Three Components That Makes Up Vitamin A. Retinol Is an Intermediate in the Vision Cycle and It Also Plays a Role in Growth and Differentiation. 
    34632   Retinol Transporter Activity  Enables the Directed Movement of Retinol Into Out of or Within a Cell or Between Cells. Retinol Is Vitamin A1 2 6 6 Trimethyl 1 (9' Hydroxy 3' 7' Dimethylnona 1' 3' 5' 7' Tetraenyl)cyclohex 1 Ene One of the Three Components That Makes Up Vitamin A. 
    36094   Small Molecule Binding  Interacting Selectively and Non Covalently with a Small Molecule Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q23.33 5950     retinol binding protein 4, plasma RBP4    

    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
    rs121918584 LS-SNP   dbSNP   A 41 I - > N Beta Ladder 2% (Buried) 10 95360496
    rs11546955 LS-SNP   dbSNP   A 54 S - > R Beta Ladder 31% (Intermediate) 10 95360456
    rs121918585 LS-SNP   dbSNP   A 75 G - > D Beta Ladder 6% (Buried) 10 95360227
    rs200867321 LS-SNP   dbSNP   A 75 G - > S Beta Ladder 6% (Buried) 10 95360228
    rs201407285 LS-SNP   dbSNP   A 81 E - > K Bend 108% (Exposed) 10 95360210
    rs149091963 LS-SNP   dbSNP   A 83 P - > L Turn 46% (Exposed) 10 95360203
    rs113069478 LS-SNP   dbSNP   A 84 A - > V Turn 0% (Buried) 10 95360200
    rs145044751 LS-SNP   dbSNP   A 88 M - > L Beta Ladder 13% (Intermediate) 10 95360189
    rs189196082 LS-SNP   dbSNP   A 145 P - > S Coil 47% (Exposed) 10 95353661
    rs139534453 LS-SNP   dbSNP   A 155 R - > W Helix 28% (Intermediate) 10 95353631
    rs150540008 LS-SNP   dbSNP   A 158 E - > D Helix 36% (Exposed) 10 95353620
    rs202087238 LS-SNP   dbSNP   A 159 L - > V Turn 3% (Buried) 10 95353619
    rs116887052 LS-SNP   dbSNP   A 164 Q - > K Bend 52% (Exposed) 10 95353604