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Crystal structure of human insulin degrading enzyme (ide) in complex with compund 41367
Biology and Chemistry Report
4DTT
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text METALLOPROTEASE, ZINC BINDING, HYDROLASE-HYDROLASE INHIBITOR COMPLEX

    Polymeric Molecules

    Chain A,B
    Description Insulin-degrading enzyme 
    Fragment UNP RESIDUES 42-1019 
    Mutation C110L,C171S,C178A,C257V,C414L,C573N,C590S,C789S,C812A,C819A,C904S,C966N,C974A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 114562.0 
    Source Method genetically manipulated  
    Entity Name Abeta-degrading protease, Insulin protease, Insulinase, Insulysin 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    I41  2-[[2-[[(2S)-3-(3H-IMIDAZOL-4-YL)-1-METHOXY-1-OXO-PROPAN-2-YL]AMINO]-2-OXO-ETHYL]-(PHENYLMETHYL)AMINO]ETHANOIC ACID  C18 H22 N4 O5   374.39  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     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.4.24.56      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 
    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. 


     
  •   Gene Details   Hide

    Genetic Source

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


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q23-q25 3416     insulin-degrading enzyme IDE    

    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 148% (Exposed) 10 94297278
    rs140287132 LS-SNP   dbSNP   A 43 N - > T Coil 148% (Exposed) 10 94297278
    rs151208561 LS-SNP   dbSNP   A 48 K - > R Beta Ladder 62% (Exposed) 10 94297263
    rs151208561 LS-SNP   dbSNP   A 48 K - > R Beta Ladder 62% (Exposed) 10 94297263
    rs142209574 LS-SNP   dbSNP   A 65 R - > Q Beta Ladder 25% (Intermediate) 10 94297212
    rs142209574 LS-SNP   dbSNP   A 65 R - > Q Beta Ladder 25% (Intermediate) 10 94297212
    rs142309020 LS-SNP   dbSNP   A 71 N - > D Turn 10% (Intermediate) 10 94297195
    rs142309020 LS-SNP   dbSNP   A 71 N - > D Turn 10% (Intermediate) 10 94297195
    rs79711272 LS-SNP   dbSNP   A 105 G - > D Turn 0% (Buried) 10 94294512
    rs79711272 LS-SNP   dbSNP   A 105 G - > D Turn 0% (Buried) 10 94294512
    rs74593235 LS-SNP   dbSNP   A 117 G - > R Coil 4% (Buried) 10 94294477
    rs74593235 LS-SNP   dbSNP   A 117 G - > R Coil 4% (Buried) 10 94294477
    rs190882251 LS-SNP   dbSNP   A 122 P - > H Coil 62% (Exposed) 10 94294461
    rs190882251 LS-SNP   dbSNP   A 122 P - > H Coil 62% (Exposed) 10 94294461
    rs181513956 LS-SNP   dbSNP   A 124 E - > K Turn 21% (Intermediate) 10 94294456
    rs181513956 LS-SNP   dbSNP   A 124 E - > K Turn 21% (Intermediate) 10 94294456
    rs188992947 LS-SNP   dbSNP   A 126 E - > K Helix 15% (Intermediate) 10 94294450
    rs188992947 LS-SNP   dbSNP   A 126 E - > K Helix 15% (Intermediate) 10 94294450
    rs184917666 LS-SNP   dbSNP   A 127 Y - > S Helix 3% (Buried) 10 94294446
    rs184917666 LS-SNP   dbSNP   A 127 Y - > S Helix 3% (Buried) 10 94294446
    rs139454255 LS-SNP   dbSNP   A 172 P - > L Beta 9% (Buried) 10 94291651
    rs139454255 LS-SNP   dbSNP   A 172 P - > L Beta 9% (Buried) 10 94291651
    rs201014275 LS-SNP   dbSNP   A 187 D - > N Helix 26% (Intermediate) 10 94291607
    rs201014275 LS-SNP   dbSNP   A 187 D - > N Helix 26% (Intermediate) 10 94291607
    rs116003953 LS-SNP   dbSNP   A 212 K - > N Turn 96% (Exposed) 10 94291530
    rs116003953 LS-SNP   dbSNP   A 212 K - > N Turn 96% (Exposed) 10 94291530
    rs139878071 LS-SNP   dbSNP   A 232 Q - > R Helix 68% (Exposed) 10 94274766
    rs139878071 LS-SNP   dbSNP   A 232 Q - > R Helix 68% (Exposed) 10 94274766
    rs200118524 LS-SNP   dbSNP   A 254 M - > T Beta Ladder 0% (Buried) 10 94274700
    rs200118524 LS-SNP   dbSNP   A 254 M - > T Beta Ladder 0% (Buried) 10 94274700
    rs181335965 LS-SNP   dbSNP   A 256 V - > G Beta Ladder 0% (Buried) 10 94274694
    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
    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
    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
    rs192563243 LS-SNP   dbSNP   A 260 G - > CS Beta Ladder 0% (Buried) 10 94274683
    rs11187039 LS-SNP   dbSNP   A 298 L - > F Bend 9% (Intermediate) 10 94269812
    rs11187039 LS-SNP   dbSNP   A 298 L - > F Bend 9% (Intermediate) 10 94269812
    rs201437960 LS-SNP   dbSNP   A 318 P - > A Beta Ladder 8% (Buried) 10 94268593
    rs201437960 LS-SNP   dbSNP   A 318 P - > A Beta Ladder 8% (Buried) 10 94268593
    rs77824934 LS-SNP   dbSNP   A 357 N - > S Beta Ladder 13% (Intermediate) 10 94267953
    rs77824934 LS-SNP   dbSNP   A 357 N - > S Beta Ladder 13% (Intermediate) 10 94267953
    rs200246238 LS-SNP   dbSNP   A 381 E - > D Helix 65% (Exposed) 10 94267880
    rs200246238 LS-SNP   dbSNP   A 381 E - > D Helix 65% (Exposed) 10 94267880
    rs200912671 LS-SNP   dbSNP   A 433 Y - > C Helix 6% (Buried) 10 94266227
    rs200912671 LS-SNP   dbSNP   A 433 Y - > C Helix 6% (Buried) 10 94266227
    rs111428437 LS-SNP   dbSNP   A 448 E - > G 3/10 Helix 25% (Intermediate) 10 94264638
    rs111428437 LS-SNP   dbSNP   A 448 E - > G 3/10 Helix 25% (Intermediate) 10 94264638
    rs34708742 LS-SNP   dbSNP   A 452 A - > V Turn 6% (Buried) 10 94264626
    rs141915194 LS-SNP   dbSNP   A 452 A - > T Turn 6% (Buried) 10 94264627
    rs141915194 LS-SNP   dbSNP   A 452 A - > T Turn 6% (Buried) 10 94264627
    rs34708742 LS-SNP   dbSNP   A 452 A - > V Turn 6% (Buried) 10 94264626
    rs143289472 LS-SNP   dbSNP   A 465 E - > A Helix 62% (Exposed) 10 94264587
    rs143289472 LS-SNP   dbSNP   A 465 E - > A Helix 62% (Exposed) 10 94264587
    rs149596491 LS-SNP   dbSNP   A 484 S - > A 3/10 Helix 45% (Exposed) 10 94250333
    rs117251230 LS-SNP   dbSNP   A 484 S - > C 3/10 Helix 45% (Exposed) 10 94250332
    rs149596491 LS-SNP   dbSNP   A 484 S - > A 3/10 Helix 45% (Exposed) 10 94250333
    rs117251230 LS-SNP   dbSNP   A 484 S - > C 3/10 Helix 45% (Exposed) 10 94250332
    rs140884087 LS-SNP   dbSNP   A 491 R - > H Beta Ladder 47% (Exposed) 10 94250311
    rs140884087 LS-SNP   dbSNP   A 491 R - > H Beta Ladder 47% (Exposed) 10 94250311
    rs150132183 LS-SNP   dbSNP   A 506 P - > L Coil 56% (Exposed) 10 94250266
    rs150132183 LS-SNP   dbSNP   A 506 P - > L Coil 56% (Exposed) 10 94250266
    rs147628298 LS-SNP   dbSNP   A 511 K - > E Helix 21% (Intermediate) 10 94250252
    rs147628298 LS-SNP   dbSNP   A 511 K - > E Helix 21% (Intermediate) 10 94250252
    rs147012131 LS-SNP   dbSNP   A 539 P - > L Coil 72% (Exposed) 10 94246993
    rs147012131 LS-SNP   dbSNP   A 539 P - > L Coil 72% (Exposed) 10 94246993
    rs142102179 LS-SNP   dbSNP   A 547 Y - > C Bend 37% (Exposed) 10 94246969
    rs142102179 LS-SNP   dbSNP   A 547 Y - > C Bend 37% (Exposed) 10 94246969
    rs113357566 LS-SNP   dbSNP   A 564 D - > G Coil 6% (Buried) 10 94243060
    rs113357566 LS-SNP   dbSNP   A 564 D - > G Coil 6% (Buried) 10 94243060
    rs5030982 LS-SNP   dbSNP   A 582 F - > L 3/10 Helix 3% (Buried) 10 94239172
    rs5030982 LS-SNP   dbSNP   A 582 F - > L 3/10 Helix 3% (Buried) 10 94239172
    rs139706336 LS-SNP   dbSNP   A 661 I - > M Helix 17% (Intermediate) 10 94235653
    rs139706336 LS-SNP   dbSNP   A 661 I - > M Helix 17% (Intermediate) 10 94235653
    rs76377051 LS-SNP   dbSNP   A 673 F - > S 3/10 Helix 18% (Intermediate) 10 94234696
    rs76377051 LS-SNP   dbSNP   A 673 F - > S 3/10 Helix 18% (Intermediate) 10 94234696
    rs146391334 LS-SNP   dbSNP   A 683 M - > V Helix 32% (Intermediate) 10 94234667
    rs146391334 LS-SNP   dbSNP   A 683 M - > V Helix 32% (Intermediate) 10 94234667
    rs142295768 LS-SNP   dbSNP   A 687 R - > C Helix 52% (Exposed) 10 94234655
    rs142295768 LS-SNP   dbSNP   A 687 R - > C Helix 52% (Exposed) 10 94234655
    rs76587725 LS-SNP   dbSNP   A 722 R - > W Beta Ladder 5% (Buried) 10 94230055
    rs76587725 LS-SNP   dbSNP   A 722 R - > W Beta Ladder 5% (Buried) 10 94230055
    rs202130657 LS-SNP   dbSNP   A 728 L - > I Beta Ladder 0% (Buried) 10 94230037
    rs202130657 LS-SNP   dbSNP   A 728 L - > I Beta Ladder 0% (Buried) 10 94230037
    rs112372000 LS-SNP   dbSNP   A 737 A - > S Helix 34% (Intermediate) 10 94228747
    rs112372000 LS-SNP   dbSNP   A 737 A - > S Helix 34% (Intermediate) 10 94228747
    rs200555551 LS-SNP   dbSNP   A 738 A - > P Helix 0% (Buried) 10 94228744
    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
    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
    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
    rs143583824 LS-SNP   dbSNP   A 792 E - > K Beta Ladder 1% (Buried) 10 94225547
    rs61736444 LS-SNP   dbSNP   A 809 E - > Q Helix 9% (Buried) 10 94225496
    rs61736444 LS-SNP   dbSNP   A 809 E - > Q Helix 9% (Buried) 10 94225496
    rs1042444 LS-SNP   dbSNP   A 845 G - > S Beta Ladder 0% (Buried) 10 94223716
    rs1042444 LS-SNP   dbSNP   A 845 G - > S Beta Ladder 0% (Buried) 10 94223716
    rs192230461 LS-SNP   dbSNP   A 868 I - > S Helix 20% (Intermediate) 10 94223646
    rs192230461 LS-SNP   dbSNP   A 868 I - > S Helix 20% (Intermediate) 10 94223646
    rs145451690 LS-SNP   dbSNP   A 878 T - > A Coil 64% (Exposed) 10 94223617
    rs145451690 LS-SNP   dbSNP   A 878 T - > A Coil 64% (Exposed) 10 94223617
    rs150078715 LS-SNP   dbSNP   A 882 F - > L Helix 0% (Buried) 10 94223603
    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
    rs140729995 LS-SNP   dbSNP   A 923 T - > I Helix 42% (Exposed) 10 94221003
    rs150947060 LS-SNP   dbSNP   A 926 A - > T Helix 60% (Exposed) 10 94220995
    rs150947060 LS-SNP   dbSNP   A 926 A - > T Helix 60% (Exposed) 10 94220995
    rs145220987 LS-SNP   dbSNP   A 936 I - > T Helix 0% (Buried) 10 94220964
    rs145220987 LS-SNP   dbSNP   A 936 I - > T Helix 0% (Buried) 10 94220964
    rs12356364 LS-SNP   dbSNP   A 947 D - > N Turn 74% (Exposed) 10 94216173
    rs12356364 LS-SNP   dbSNP   A 947 D - > N Turn 74% (Exposed) 10 94216173
    rs201349668 LS-SNP   dbSNP   A 978 I - > V Coil 79% (Exposed) 10 94215365
    rs201349668 LS-SNP   dbSNP   A 978 I - > V Coil 79% (Exposed) 10 94215365
    rs188614842 LS-SNP   dbSNP   A 982 Q - > K Coil 79% (Exposed) 10 94215353
    rs188614842 LS-SNP   dbSNP   A 982 Q - > K Coil 79% (Exposed) 10 94215353