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CRYSTAL STRUCTURE OF HUMAN INSULIN DEGRADING ENZYME IN COMPLEX WITH IODINATED INSULIN
Biology and Chemistry Report
2WC0
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HORMONE
    Text HYDROLASE/HORMONE, DIOXANE, INSULIN, HORMONE, PROTEASE, SECRETED, HUMAN INSULIN-DEGRADING ENZYME, DISULFIDE BOND, METALLOPROTEASE, GLUCOSE METABOLISM, CARBOHYDRATE METABOLISM, HYDROLASE, METAL-BINDING, CLEAVAGE ON PAIR OF BASIC RESIDUES, HYDROLASE-HORMONE complex

    Polymeric Molecules

    Chain A,B
    Description INSULIN-DEGRADING ENZYME 
    Fragment RESIDUES 42-1019 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 114562.0 
    Source Method genetically manipulated  
    Entity Name INSULIN PROTEASE, INSULYSIN, INSULINASE 
    Chain C,E
    Description INSULIN A CHAIN 
    Fragment RESIDUES 90-110 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 2383.7 
    Source Method synthetic  
    Chain D,F
    Description INSULIN B CHAIN 
    Fragment RESIDUES 25-54 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 3434.0 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    DIO  1,4-DIETHYLENE DIOXIDE  C4 H8 O2   88.11  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B IDE_HUMAN B2R721     
    C,E INS_HUMAN P01308     
    D,F INS_HUMAN P01308     

    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 B  3.4.24.56        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6200   ATP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    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. 
    8286   Insulin Receptor Signaling Pathway  The Series of Molecular Signals Generated As a Consequence of the Insulin Receptor Binding to Insulin. 
    8340   Determination of Adult Lifespan  The Control of Viability and Duration in the Adult Phase of the Life Cycle. 
    10815   Bradykinin Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of the Peptide Bradykinin. 
    10992   Ubiquitin Homeostasis  Any Process Involved in the Maintenance of an Internal Steady State of Ubiquitin Monomers and Free Ubiquitin Chains At the Level of the Cell. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    32461   Positive Regulation of Protein Oligomerization  Any Process That Activates or Increases the Frequency Rate or Extent of Protein Oligomerization. 
    42447   Hormone Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Any Hormone Naturally Occurring Substances Secreted by Specialized Cells That Affects the Metabolism or Behavior of Other Cells Possessing Functional Receptors For the Hormone. 
    44257   Cellular Protein Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Protein by Individual Cells. 
    45861   Negative Regulation of Proteolysis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Hydrolysis of a Peptide Bond or Bonds Within a Protein. 
    50435   Beta Amyloid Metabolic Process  The Chemical Reactions and Pathways Involving Beta Amyloid a Glycoprotein Associated with Alzheimer's Disease and Its Precursor Amyloid Precursor Protein (app). 
    51260   Protein Homooligomerization  The Process of Creating Protein Oligomers Compounds Composed of a Small Number Usually Between Three and Ten of Identical Component Monomers. Oligomers May Be Formed by the Polymerization of a Number of Monomers or the Depolymerization of a Large Protein Polymer. 
    51289   Protein Homotetramerization  The Formation of a Protein Homotetramer a Macromolecular Structure Consisting of Four Noncovalently Associated Identical Subunits. 
    51291   Protein Heterooligomerization  The Process of Creating Protein Oligomers Compounds Composed of a Small Number Usually Between Three and Ten of Component Monomers That Are Not All Identical. Oligomers May Be Formed by the Polymerization of a Number of Monomers or the Depolymerization of a Large Protein Polymer. 
    51603   Proteolysis Involved in Cellular Protein Catabolic Process  The Hydrolysis of a Peptide Bond or Bonds Within a Protein As Part of the Chemical Reactions and Pathways Resulting in the Breakdown of a Protein by Individual Cells. 
    1901142   Insulin Metabolic Process  The Chemical Reactions and Pathways Involving Insulin. 
    1901143   Insulin Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Insulin. 
    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. 
    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. 
    5739   Mitochondrion  A Semiautonomous Self Replicating Organelle That Occurs in Varying Numbers Shapes and Sizes in the Cytoplasm of Virtually All Eukaryotic Cells. It Is Notably the Site of Tissue Respiration. 
    5777   Peroxisome  A Small Organelle Enclosed by a Single Membrane and Found in Most Eukaryotic Cells. Contains Peroxidases and Other Enzymes Involved in a Variety of Metabolic Processes Including Free Radical Detoxification Lipid Catabolism and Biosynthesis and Hydrogen Peroxide Metabolism. 
    5782   Peroxisomal Matrix  The Volume Contained Within the Membranes of a Peroxisome; in Many Cells the Matrix Contains a Crystalloid Core Largely Composed of Urate Oxidase. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    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. 
    9986   Cell Surface  The External Part of the Cell Wall And/or Plasma Membrane. 
    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. 
    31597   Cytosolic Proteasome Complex  A Proteasome Complex Found in the Cytosol of a Cell. 
    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. 
    1540   Beta Amyloid Binding  Interacting Selectively and Non Covalently with Beta Amyloid Peptide/protein And/or Its Precursor. 
    1948   Glycoprotein Binding  Interacting Selectively and Non Covalently with a Glycoprotein a Protein That Contains Covalently Bound Glycose (monosaccharide) Residues. These Also Include Proteoglycans. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4222   Metalloendopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Mechanism in Which Water Acts As a Nucleophile One or Two Metal Ions Hold the Water Molecule in Place and Charged Amino Acid Side Chains Are Ligands For the Metal Ions. 
    5102   Receptor Binding  Interacting Selectively and Non Covalently with One or More Specific Sites On a Receptor Molecule a Macromolecule That Undergoes Combination with a Hormone Neurotransmitter Drug or Intracellular Messenger to Initiate a Change in Cell Function. 
    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. 
    8233   Peptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond. a Peptide Bond Is a Covalent Bond Formed When the Carbon Atom From the Carboxyl Group of One Amino Acid Shares Electrons with the Nitrogen Atom From the Amino Group of a Second Amino Acid. 
    8237   Metallopeptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds by a Mechanism in Which Water Acts As a Nucleophile One or Two Metal Ions Hold the Water Molecule in Place and Charged Amino Acid Side Chains Are Ligands For the Metal Ions. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16887   Atpase Activity  Catalysis of the Reaction: ATP + H2o = Adp + Phosphate + 2 H+. May or May Not Be Coupled to Another Reaction. 
    17046   Peptide Hormone Binding  Interacting Selectively and Non Covalently with Any Peptide with Hormonal Activity in Animals. 
    31626   Beta Endorphin Binding  Interacting Selectively and Non Covalently with Beta Endorphin a Peptide Generated by the Cleavage of Pro Opiomelanocortin. 
    42277   Peptide Binding  Interacting Selectively and Non Covalently with Peptides Any of a Group of Organic Compounds Comprising Two or More Amino Acids Linked by Peptide Bonds. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 
    43130   Ubiquitin Binding  Interacting Selectively and Non Covalently with Ubiquitin a Protein That When Covalently Bound to Other Cellular Proteins Marks Them For Proteolytic Degradation. 
    43559   Insulin Binding  Interacting Selectively and Non Covalently with Insulin a Polypeptide Hormone Produced by the Islets of Langerhans of the Pancreas in Mammals and by the Homologous Organs of Other Organisms. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain C,E
    GO ID   Ontology GO Term Definition
    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. 
    5179   Hormone Activity  The Action Characteristic of a Hormone Any Substance Formed in Very Small Amounts in One Specialized Organ or Group of Cells and Carried (sometimes in the Bloodstream) to Another Organ or Group of Cells in the Same Organism Upon Which It Has a Specific Regulatory Action. the Term Was Originally Applied to Agents with a Stimulatory Physiological Action in Vertebrate Animals (as Opposed to a Chalone Which Has a Depressant Action). Usage Is Now Extended to Regulatory Compounds in Lower Animals and Plants and to Synthetic Substances Having Comparable Effects; All Bind Receptors and Trigger Some Biological Process. 
    Chain D,F
    GO ID   Ontology GO Term Definition
    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. 
    5179   Hormone Activity  The Action Characteristic of a Hormone Any Substance Formed in Very Small Amounts in One Specialized Organ or Group of Cells and Carried (sometimes in the Bloodstream) to Another Organ or Group of Cells in the Same Organism Upon Which It Has a Specific Regulatory Action. the Term Was Originally Applied to Agents with a Stimulatory Physiological Action in Vertebrate Animals (as Opposed to a Chalone Which Has a Depressant Action). Usage Is Now Extended to Regulatory Compounds in Lower Animals and Plants and to Synthetic Substances Having Comparable Effects; All Bind Receptors and Trigger Some Biological Process. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q23-q25 3416     insulin-degrading enzyme IDE    
    11 11p15.5 3630     insulin INS    

    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
    rs140287132 LS-SNP   dbSNP   A 43 N - > T Coil 133% (Exposed) 10 94297278
    rs151208561 LS-SNP   dbSNP   A 48 K - > R Beta Ladder 54% (Exposed) 10 94297263
    rs142209574 LS-SNP   dbSNP   A 65 R - > Q Beta Ladder 25% (Intermediate) 10 94297212
    rs142309020 LS-SNP   dbSNP   A 71 N - > D Turn 12% (Intermediate) 10 94297195
    rs79711272 LS-SNP   dbSNP   A 105 G - > D Turn 0% (Buried) 10 94294512
    rs74593235 LS-SNP   dbSNP   A 117 G - > R Coil 7% (Buried) 10 94294477
    rs190882251 LS-SNP   dbSNP   A 122 P - > H Coil 42% (Exposed) 10 94294461
    rs181513956 LS-SNP   dbSNP   A 124 E - > K Turn 19% (Intermediate) 10 94294456
    rs188992947 LS-SNP   dbSNP   A 126 E - > K Helix 3% (Buried) 10 94294450
    rs184917666 LS-SNP   dbSNP   A 127 Y - > S Helix 5% (Buried) 10 94294446
    rs139454255 LS-SNP   dbSNP   A 172 P - > L Beta 7% (Buried) 10 94291651
    rs201014275 LS-SNP   dbSNP   A 187 D - > N Helix 20% (Intermediate) 10 94291607
    rs116003953 LS-SNP   dbSNP   A 212 K - > N Turn 91% (Exposed) 10 94291530
    rs139878071 LS-SNP   dbSNP   A 232 Q - > R Helix 65% (Exposed) 10 94274766
    rs200118524 LS-SNP   dbSNP   A 254 M - > T Beta Ladder 1% (Buried) 10 94274700
    rs181335965 LS-SNP   dbSNP   A 256 V - > G Beta Ladder 0% (Buried) 10 94274694
    rs189181823 LS-SNP   dbSNP   A 257 C - > F Beta Ladder 0% (Buried) 10 94274691
    rs184283936 LS-SNP   dbSNP   A 259 L - > F Beta Ladder 1% (Buried) 10 94274684
    rs192563243 LS-SNP   dbSNP   A 260 G - > CS Beta Ladder 0% (Buried) 10 94274683
    rs11187039 LS-SNP   dbSNP   A 298 L - > F Bend 15% (Intermediate) 10 94269812
    rs201437960 LS-SNP   dbSNP   A 318 P - > A Beta Ladder 9% (Buried) 10 94268593
    rs77824934 LS-SNP   dbSNP   A 357 N - > S Bend 13% (Intermediate) 10 94267953
    rs200246238 LS-SNP   dbSNP   A 381 E - > D Helix 60% (Exposed) 10 94267880
    rs200912671 LS-SNP   dbSNP   A 433 Y - > C Helix 7% (Buried) 10 94266227
    rs111428437 LS-SNP   dbSNP   A 448 E - > G 3/10 Helix 26% (Intermediate) 10 94264638
    rs141915194 LS-SNP   dbSNP   A 452 A - > T Turn 7% (Buried) 10 94264627
    rs34708742 LS-SNP   dbSNP   A 452 A - > V Turn 7% (Buried) 10 94264626
    rs143289472 LS-SNP   dbSNP   A 465 E - > A Helix 68% (Exposed) 10 94264587
    rs149596491 LS-SNP   dbSNP   A 484 S - > A 3/10 Helix 54% (Exposed) 10 94250333
    rs117251230 LS-SNP   dbSNP   A 484 S - > C 3/10 Helix 54% (Exposed) 10 94250332
    rs140884087 LS-SNP   dbSNP   A 491 R - > H Beta Ladder 44% (Exposed) 10 94250311
    rs150132183 LS-SNP   dbSNP   A 506 P - > L Coil 54% (Exposed) 10 94250266 DIO
    rs147628298 LS-SNP   dbSNP   A 511 K - > E Helix 45% (Exposed) 10 94250252
    rs147012131 LS-SNP   dbSNP   A 539 P - > L Coil 77% (Exposed) 10 94246993
    rs142102179 LS-SNP   dbSNP   A 547 Y - > C Bend 35% (Intermediate) 10 94246969
    rs113357566 LS-SNP   dbSNP   A 564 D - > G Coil 7% (Buried) 10 94243060
    rs5030982 LS-SNP   dbSNP   A 582 F - > L 3/10 Helix 31% (Intermediate) 10 94239172
    rs139706336 LS-SNP   dbSNP   A 661 I - > M Helix 13% (Intermediate) 10 94235653
    rs76377051 LS-SNP   dbSNP   A 673 F - > S 3/10 Helix 21% (Intermediate) 10 94234696
    rs146391334 LS-SNP   dbSNP   A 683 M - > V Helix 16% (Intermediate) 10 94234667
    rs142295768 LS-SNP   dbSNP   A 687 R - > C Helix 43% (Exposed) 10 94234655
    rs76587725 LS-SNP   dbSNP   A 722 R - > W Beta 40% (Exposed) 10 94230055
    rs202130657 LS-SNP   dbSNP   A 728 L - > I Beta Ladder 0% (Buried) 10 94230037
    rs112372000 LS-SNP   dbSNP   A 737 A - > S Helix 36% (Intermediate) 10 94228747
    rs200555551 LS-SNP   dbSNP   A 738 A - > P Helix 0% (Buried) 10 94228744
    rs114285269 LS-SNP   dbSNP   A 742 M - > T Helix 0% (Buried) 10 94228731
    rs35640611 LS-SNP   dbSNP   A 791 I - > M Beta Ladder 1% (Buried) 10 94225548
    rs143583824 LS-SNP   dbSNP   A 792 E - > K Beta Ladder 1% (Buried) 10 94225547
    rs61736444 LS-SNP   dbSNP   A 809 E - > Q Helix 10% (Intermediate) 10 94225496
    rs1042444 LS-SNP   dbSNP   A 845 G - > S Beta Ladder 0% (Buried) 10 94223716
    rs192230461 LS-SNP   dbSNP   A 868 I - > S Helix 34% (Intermediate) 10 94223646
    rs145451690 LS-SNP   dbSNP   A 878 T - > A Coil 6% (Buried) 10 94223617
    rs150078715 LS-SNP   dbSNP   A 882 F - > L Helix 0% (Buried) 10 94223603
    rs140729995 LS-SNP   dbSNP   A 923 T - > I Helix 42% (Exposed) 10 94221003
    rs150947060 LS-SNP   dbSNP   A 926 A - > T Helix 61% (Exposed) 10 94220995
    rs145220987 LS-SNP   dbSNP   A 936 I - > T Helix 0% (Buried) 10 94220964
    rs12356364 LS-SNP   dbSNP   A 947 D - > N Turn 80% (Exposed) 10 94216173
    rs188614842 LS-SNP   dbSNP   A 982 Q - > K Coil 83% (Exposed) 10 94215353
    rs80356670 LS-SNP   dbSNP   C 1 G - > C Coil 11% (Intermediate) 11 2181147
    rs121918102 LS-SNP   dbSNP   C 3 V - > L Coil 13% (Intermediate) 11 2181141
    rs193929388 LS-SNP   dbSNP   C 7 C - > Y Helix 0% (Buried) 11 2181128
    rs80356671 LS-SNP   dbSNP   C 7 C - > S Helix 0% (Buried) 11 2181128
    rs121908276 LS-SNP   dbSNP   C 12 S - > C Coil 0% (Buried) 11 2181113
    rs121908277 LS-SNP   dbSNP   C 14 Y - > C Helix 9% (Intermediate) 11 2181107
    rs80356672 LS-SNP   dbSNP   C 19 Y - > C Turn 49% (Exposed) 11 2181092