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CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP-BIR2 AND CASPASE 3
Biology and Chemistry Report
1I3O
  •   Structure Details   Hide

    Structure Keywords

    Keywords APOPTOSIS
    Text complex, IAP, caspase, Apoptosis

    Polymeric Molecules

    Chain A,C
    Description CASPASE 3 
    Fragment APOPAIN P17 SUBUNIT 
    Mutation C285A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19727.4 
    Source Method genetically manipulated  
    Chain B,D
    Description CASPASE 3 
    Fragment APOPAIN P12 SUBUNIT 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 12981.9 
    Source Method genetically manipulated  
    Chain E,F
    Description BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4 
    Fragment XIAP-BIR2 
    Mutation C202A, C213G 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13993.7 
    Source Method genetically manipulated  
    Entity Name X-LINKED IAP 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C CASP3_HUMAN P42574     
    B,D CASP3_HUMAN P42574     
    E,F XIAP_HUMAN D3DTF2     

    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 C  3.4.22.56        
    B D  3.4.22.56        
    E F  6.3.2        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    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. 
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    4197   Cysteine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Mechanism in Which the Sulfhydryl Group of a Cysteine Residue At the Active Center Acts As a Nucleophile. 
    8234   Cysteine Type Peptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds in a Polypeptide Chain by a Mechanism in Which the Sulfhydryl Group of a Cysteine Residue At the Active Center Acts As a Nucleophile. 
    Chain B,D
    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. 
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    4197   Cysteine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Mechanism in Which the Sulfhydryl Group of a Cysteine Residue At the Active Center Acts As a Nucleophile. 
    8234   Cysteine Type Peptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds in a Polypeptide Chain by a Mechanism in Which the Sulfhydryl Group of a Cysteine Residue At the Active Center Acts As a Nucleophile. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain E,F
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene u32974
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PET15B


    Chain B,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene i39005
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PET23B


    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene i39005
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PET23B


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    4 4q34 836     caspase 3, apoptosis-related cysteine peptidase CASP3    
    X Xq25 331     X-linked inhibitor of apoptosis XIAP    

    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
    rs139792606 LS-SNP   dbSNP   A 164 I - > V Beta Ladder 0% (Buried) 4 185556484
    rs146079573 LS-SNP   dbSNP   A 166 I - > L Beta Ladder 1% (Buried) 4 185556478
    rs201901370 LS-SNP   dbSNP   A 196 N - > D Turn 15% (Intermediate) 4 185553491
    rs199988965 LS-SNP   dbSNP   A 196 N - > S Turn 15% (Intermediate) 4 185553490
    rs111512673 LS-SNP   dbSNP   A 207 L - > P Coil 15% (Intermediate) 4 185553457
    rs139516222 LS-SNP   dbSNP   A 216 M - > V Helix 40% (Exposed) 4 185553431
    rs146285839 LS-SNP   dbSNP   A 217 R - > H Helix 52% (Exposed) 4 185553427
    rs78678473 LS-SNP   dbSNP   A 233 V - > A Beta Ladder 0% (Buried) 4 185553052
    rs28382722 LS-SNP   dbSNP   E 133 S - > F Turn 98% (Exposed) X 123019910
    rs150317928 LS-SNP   dbSNP   E 152 T - > S 3/10 Helix 63% (Exposed) X 123019967
    rs138049858 LS-SNP   dbSNP   E 202 C - > S Turn 0% (Buried) X 123020117 ZN
    rs140973844 LS-SNP   dbSNP   E 228 F - > C Helix 6% (Buried) X 123020195
    rs144884904 LS-SNP   dbSNP   E 230 V - > I Helix 22% (Intermediate) X 123020200 ZN