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Crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 ERAP1
Biology and Chemistry Report
3QNF
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text Structural Genomics Consortium, SGC, glycoprotein, metal-binding, metalloprotease, protease, adaptive immunity, HYDROLASE

    Polymeric Molecules

    Chain A,B,C
    Description Endoplasmic reticulum aminopeptidase 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 109072.0 
    Source Method genetically manipulated  
    Entity Name ARTS-1, Adipocyte-derived leucine aminopeptidase, A-LAP, Aminopeptidase PILS, Puromycin-insensitive leucyl-specific aminopeptidase, PILS-AP, Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MAN  ALPHA-D-MANNOSE  C6 H12 O6   180.16  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C ERAP1_HUMAN O60278     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C  3.4.11      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C
    GO ID   Ontology GO Term Definition
    1525   Angiogenesis  Blood Vessel Formation When New Vessels Emerge From the Proliferation of Pre Existing Blood Vessels. 
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    2474   Antigen Processing and Presentation of Peptide Antigen Via Mhc Class I  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen On Its Cell Surface in Association with an Mhc Class I Protein Complex. Class I Here Refers to Classical Class I Molecules. 
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    6509   Membrane Protein Ectodomain Proteolysis  The Proteolytic Cleavage of Transmembrane Proteins and Release of Their Ectodomain (extracellular Domain). 
    8217   Regulation of Blood Pressure  Any Process That Modulates the Force with Which Blood Travels Through the Circulatory System. the Process Is Controlled by a Balance of Processes That Increase Pressure and Decrease Pressure. 
    9617   Response to Bacterium  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 From a Bacterium. 
    19885   Antigen Processing and Presentation of Endogenous Peptide Antigen Via Mhc Class I  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen of Endogenous Origin On Its Cell Surface in Association with an Mhc Class I Protein Complex. the Peptide Antigen Is Typically But Not Always Processed From a Whole Protein. Class I Here Refers to Classical Class I Molecules. 
    45088   Regulation of Innate Immune Response  Any Process That Modulates the Frequency Rate or Extent of the Innate Immune Response the Organism's First Line of Defense Against Infection. 
    45444   Fat Cell Differentiation  The Process in Which a Relatively Unspecialized Cell Acquires Specialized Features of an Adipocyte an Animal Connective Tissue Cell Specialized For the Synthesis and Storage of Fat. 
    45766   Positive Regulation of Angiogenesis  Any Process That Activates or Increases Angiogenesis. 
    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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5788   Endoplasmic Reticulum Lumen  The Volume Enclosed by the Membranes of the Endoplasmic Reticulum. 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    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. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    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. 
    4177   Aminopeptidase Activity  Catalysis of the Hydrolysis of N Terminal Amino Acid Residues From in a Polypeptide Chain. 
    5138   Interleukin 6 Receptor Binding  Interacting Selectively and Non Covalently with the Interleukin 6 Receptor. 
    5151   Interleukin 1 Type Ii Receptor Binding  Interacting Selectively and Non Covalently with a Type Ii Interleukin 1 Receptor. 
    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). 
    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. 
    8235   Metalloexopeptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond Not More Than Three Residues From the N or C Terminus of 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. 
    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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene erap1, appils, arts1, kiaa0525, unq584/pro1154
    Host Common Name Cabbage Looper
    Host Scientific Name Trichoplusia ni  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q15 51752     endoplasmic reticulum aminopeptidase 1 ERAP1    

    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
    rs3734016 LS-SNP   dbSNP   A 56 E - > K Turn 86% (Exposed) 5 96139464
    rs138846351 LS-SNP   dbSNP   A 68 H - > Y Beta Ladder 33% (Intermediate) 5 96139428 MAN,NAG
    rs151040768 LS-SNP   dbSNP   A 79 T - > A Beta Ladder 23% (Intermediate) 5 96139395
    rs26653 LS-SNP   dbSNP   A 127 R - > P 3/10 Helix 38% (Exposed) 5 96139250
    rs147823699 LS-SNP   dbSNP   A 132 A - > V Beta Ladder 0% (Buried) 5 96139235
    rs149653730 LS-SNP   dbSNP   A 142 G - > R Turn 67% (Exposed) 5 96139206
    rs140515309 LS-SNP   dbSNP   A 144 P - > L Beta Ladder 68% (Exposed) 5 96139199
    rs201670295 LS-SNP   dbSNP   A 154 N - > S Beta Ladder 78% (Exposed) 5 96139169
    rs201066303 LS-SNP   dbSNP   A 156 S - > W Beta 13% (Intermediate) 5 96139163
    rs149909757 LS-SNP   dbSNP   A 161 G - > R Beta Ladder 0% (Buried) 5 96139149
    rs141992697 LS-SNP   dbSNP   A 175 R - > W Beta Ladder 32% (Intermediate) 5 96139107
    rs142482678 LS-SNP   dbSNP   A 184 P - > R Turn 37% (Exposed) 5 96136677
    rs139782060 LS-SNP   dbSNP   A 187 A - > G 3/10 Helix 0% (Buried) 5 96136668
    rs146396644 LS-SNP   dbSNP   A 199 F - > C Bend 9% (Intermediate) 5 96136632
    rs200284630 LS-SNP   dbSNP   A 205 I - > V Beta Ladder 2% (Buried) 5 96136615
    rs112160177 LS-SNP   dbSNP   A 219 M - > T Bend 6% (Buried) 5 96136572
    rs142097626 LS-SNP   dbSNP   A 220 P - > L Coil 32% (Intermediate) 5 96136569
    rs143271510 LS-SNP   dbSNP   A 259 K - > E Beta Ladder 42% (Exposed) 5 96132901
    rs149597747 LS-SNP   dbSNP   A 265 V - > I Coil 8% (Buried) 5 96132883
    rs26618 LS-SNP   dbSNP   A 276 I - > M 3/10 Helix 13% (Intermediate) 5 96130836
    rs112686030 LS-SNP   dbSNP   A 284 D - > N Helix 44% (Exposed) 5 96130814
    rs118132132 LS-SNP   dbSNP   A 299 I - > L Bend 12% (Intermediate) 5 96130769
    rs27895 LS-SNP   dbSNP   A 346 G - > D Helix 38% (Exposed) 5 96129543
    rs2287987 LS-SNP   dbSNP   A 349 M - > V Helix 7% (Buried) 5 96129535
    rs113607082 LS-SNP   dbSNP   A 358 Q - > E Helix 0% (Buried) 5 96129508
    rs181668902 LS-SNP   dbSNP   A 406 D - > N Helix 64% (Exposed) 5 96127868
    rs145458413 LS-SNP   dbSNP   A 406 D - > E Helix 64% (Exposed) 5 96127866
    rs111453713 LS-SNP   dbSNP   A 423 V - > A Coil 37% (Exposed) 5 96127816
    rs139815574 LS-SNP   dbSNP   A 425 N - > D Coil 94% (Exposed) 5 96127811
    rs184320964 LS-SNP   dbSNP   A 447 M - > V Helix 4% (Buried) 5 96126328
    rs140121905 LS-SNP   dbSNP   A 454 A - > T Helix 37% (Exposed) 5 96126307
    rs150674566 LS-SNP   dbSNP   A 456 A - > T Helix 32% (Intermediate) 5 96126301
    rs141891516 LS-SNP   dbSNP   A 458 K - > E Helix 25% (Intermediate) 5 96126295
    rs199837380 LS-SNP   dbSNP   A 485 I - > V Coil 49% (Exposed) 5 96126070
    rs30187 LS-SNP   dbSNP   A 528 K - > R Coil 12% (Intermediate) 5 96124330
    rs142305981 LS-SNP   dbSNP   A 538 R - > K Beta Ladder 59% (Exposed) 5 96124300
    rs10050860 LS-SNP   dbSNP   A 575 D - > N Coil 93% (Exposed) 5 96122210
    rs6863093 LS-SNP   dbSNP   A 575 D - > G Coil 93% (Exposed) 5 96122209
    rs114703312 LS-SNP   dbSNP   A 588 V - > G Beta Ladder 36% (Intermediate) 5 96121672
    rs189721036 LS-SNP   dbSNP   A 603 G - > S 3/10 Helix 12% (Intermediate) 5 96121628
    rs146434826 LS-SNP   dbSNP   A 606 G - > D Bend 10% (Intermediate) 5 96121618
    rs76433375 LS-SNP   dbSNP   A 610 V - > L Beta Ladder 0% (Buried) 5 96121607
    rs149374891 LS-SNP   dbSNP   A 613 E - > D Turn 40% (Exposed) 5 96121596
    rs201856260 LS-SNP   dbSNP   A 618 D - > Y Helix 45% (Exposed) 5 96121583
    rs143881089 LS-SNP   dbSNP   A 620 L - > F Helix 1% (Buried) 5 96121575
    rs144333828 LS-SNP   dbSNP   A 636 R - > Q Helix 5% (Buried) 5 96121528
    rs111363347 LS-SNP   dbSNP   A 647 V - > I Helix 10% (Intermediate) 5 96121496
    rs147252760 LS-SNP   dbSNP   A 649 I - > T Turn 28% (Intermediate) 5 96119782
    rs201253143 LS-SNP   dbSNP   A 655 E - > K Helix 39% (Exposed) 5 96119765
    rs143726979 LS-SNP   dbSNP   A 663 Y - > C 3/10 Helix 2% (Buried) 5 96119740
    rs138598123 LS-SNP   dbSNP   A 711 I - > T Helix 8% (Buried) 5 96118908
    rs201469459 LS-SNP   dbSNP   A 713 K - > Q Helix 45% (Exposed) 5 96118903
    rs17482078 LS-SNP   dbSNP   A 725 R - > Q Helix 28% (Intermediate) 5 96118866
    rs112266389 LS-SNP   dbSNP   A 727 L - > P Helix 13% (Intermediate) 5 96118860
    rs201805082 LS-SNP   dbSNP   A 728 R - > Q Helix 14% (Intermediate) 5 96118857
    rs27044 LS-SNP   dbSNP   A 730 Q - > E Helix 35% (Intermediate) 5 96118852
    rs200156544 LS-SNP   dbSNP   A 736 C - > W Turn 26% (Intermediate) 5 96118832
    rs202045893 LS-SNP   dbSNP   A 749 G - > S Helix 32% (Intermediate) 5 96118795
    rs145659288 LS-SNP   dbSNP   A 755 K - > N Turn 37% (Exposed) 5 96118775
    rs139576768 LS-SNP   dbSNP   A 915 I - > T Coil 74% (Exposed) 5 96112182
    rs200883678 LS-SNP   dbSNP   A 920 G - > S Helix 46% (Exposed) 5 96112168