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Crystal Structure of a Truncated Soluble form of Human CD73 with Ecto-5'-Nucleotidase activity
Biology and Chemistry Report
4H1S
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text 5'-nucleotidase, HYDROLASE

    Polymeric Molecules

    Chain A,B
    Description 5'-nucleotidase 
    Fragment UNP residues 27-549 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 59044.8 
    Source Method natural source  
    Entity Name 5'-NT, Ecto-5'-nucleotidase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B 5NTD_HUMAN P21589     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.1.3.5      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6144   Purine Nucleobase Metabolic Process  The Chemical Reactions and Pathways Involving Purine Nucleobases One of the Two Classes of Nitrogen Containing Ring Compounds Found in DNA and RNA Which Include Adenine and Guanine. 
    6164   Purine Nucleotide Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of a Purine Nucleotide a Compound Consisting of Nucleoside (a Purine Base Linked to a Deoxyribose or Ribose Sugar) Esterified with a Phosphate Group At Either the 3' or 5' Hydroxyl Group of the Sugar. 
    6195   Purine Nucleotide Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Purine Nucleotide a Compound Consisting of Nucleoside (a Purine Base Linked to a Deoxyribose or Ribose Sugar) Esterified with a Phosphate Group At Either the 3' or 5' Hydroxyl Group of the Sugar. 
    6196   AMP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of AMP Adenosine Monophosphate. 
    6206   Pyrimidine Nucleobase Metabolic Process  The Chemical Reactions and Pathways Involving Pyrimidine Nucleobases 1 3 Diazine Organic Nitrogenous Bases. 
    6259   DNA Metabolic Process  Any Cellular Metabolic Process Involving Deoxyribonucleic Acid. This Is One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or More Commonly Two Strands of Linked Deoxyribonucleotides. 
    7159   Leukocyte Cell Cell Adhesion  The Attachment of a Leukocyte to Another Cell Via Adhesion Molecules. 
    7420   Brain Development  The Process Whose Specific Outcome Is the Progression of the Brain Over Time From Its Formation to the Mature Structure. Brain Development Begins with Patterning Events in the Neural Tube and Ends with the Mature Structure That Is the Center of Thought and Emotion. the Brain Is Responsible For the Coordination and Control of Bodily Activities and the Interpretation of Information From the Senses (sight Hearing Smell Etc.). 
    9166   Nucleotide Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Nucleotides Any Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Glycose Moiety; May Be Mono Di or Triphosphate; This Definition Includes Cyclic Nucleotides (nucleoside Cyclic Phosphates). 
    10044   Response to Aluminum Ion  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 Aluminum Ion Stimulus. 
    16311   Dephosphorylation  The Process of Removing One or More Phosphoric (ester or Anhydride) Residues From a Molecule. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46085   Adenosine Metabolic Process  The Chemical Reactions and Pathways Involving Adenosine Adenine Riboside a Ribonucleoside Found Widely Distributed in Cells of Every Type As the Free Nucleoside and in Combination in Nucleic Acids and Various Nucleoside Coenzymes. 
    46086   Adenosine Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Adenosine Adenine Riboside a Ribonucleoside Found Widely Distributed in Cells of Every Type As the Free Nucleoside and in Combination in Nucleic Acids and Various Nucleoside Coenzymes. 
    46135   Pyrimidine Nucleoside Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of One of a Family of Organic Molecules Consisting of a Pyrimidine Base Covalently Bonded to a Sugar Ribose (a Ribonucleoside) or Deoxyribose (a Deoxyribonucleoside). 
    46889   Positive Regulation of Lipid Biosynthetic Process  Any Process That Activates or Increases the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Lipids. 
    50728   Negative Regulation of Inflammatory Response  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Inflammatory Response. 
    55086   Nucleobase Containing Small Molecule Metabolic Process  The Cellular Chemical Reactions and Pathways Involving a Nucleobase Containing Small Molecule: a Nucleobase a Nucleoside or a Nucleotide. 
    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. 
    9986   Cell Surface  The External Part of the Cell Wall And/or Plasma Membrane. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    31225   Anchored Component of Membrane  The Component of a Membrane Consisting of the Gene Products That Are Tethered to the Membrane Only by a Covalently Attached Anchor Such As a Lipid Group That Is Embedded in the Membrane. Gene Products with Peptide Sequences That Are Embedded in the Membrane Are Excluded From This Grouping. 
    70062   Extracellular 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. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    97060   Synaptic Membrane  A Specialized Area of Membrane On Either the Presynaptic or the Postsynaptic Side of a Synapse the Junction Between a Nerve Fiber of One Neuron and Another Neuron or Muscle Fiber or Glial 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. 
    8198   Ferrous Iron Binding  Interacting Selectively and Non Covalently with Ferrous Iron Fe(ii). 
    8253   5' Nucleotidase Activity  Catalysis of the Reaction: a 5' Ribonucleotide + H2o = a Ribonucleoside + Phosphate. 
    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. 
    16788   Hydrolase Activity Acting On Ester Bonds  Catalysis of the Hydrolysis of Any Ester Bond. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Natural Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6q14-q21 4907     5'-nucleotidase, ecto (CD73) NT5E    

    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
    rs200250022 LS-SNP   dbSNP   A 62 A - > S Helix 2% (Buried) 6 86160041
    rs200207416 LS-SNP   dbSNP   A 134 E - > Q Turn 60% (Exposed) 6 86176838
    rs200369370 LS-SNP   dbSNP   A 153 Q - > E Helix 34% (Intermediate) 6 86176895
    rs199573247 LS-SNP   dbSNP   A 181 T - > N Helix 0% (Buried) 6 86176980
    rs201534865 LS-SNP   dbSNP   A 202 P - > H Helix 54% (Exposed) 6 86180997
    rs144535109 LS-SNP   dbSNP   A 228 L - > F Helix 40% (Exposed) 6 86181074
    rs141370047 LS-SNP   dbSNP   A 234 R - > S Turn 52% (Exposed) 6 86181094
    rs200664520 LS-SNP   dbSNP   A 235 G - > S Turn 17% (Intermediate) 6 86181095
    rs200840390 LS-SNP   dbSNP   A 239 V - > M Beta Ladder 0% (Buried) 6 86181107
    rs201657741 LS-SNP   dbSNP   A 240 V - > M Beta Ladder 0% (Buried) 6 86181110
    rs184831134 LS-SNP   dbSNP   A 269 S - > P Coil 5% (Buried) 6 86195006
    rs41271617 LS-SNP   dbSNP   A 278 V - > I Beta Ladder 0% (Buried) 6 86195033
    rs148199616 LS-SNP   dbSNP   A 300 V - > I Beta Ladder 27% (Intermediate) 6 86195099
    rs201782026 LS-SNP   dbSNP   A 308 I - > T Beta Ladder 24% (Intermediate) 6 86195124
    rs147019457 LS-SNP   dbSNP   A 327 W - > R Helix 21% (Intermediate) 6 86197082
    rs2229522 LS-SNP   dbSNP   A 347 D - > E Coil 16% (Intermediate) 6 86197144
    rs200648774 LS-SNP   dbSNP   A 354 R - > C Turn 13% (Intermediate) 6 86197163 PO4
    rs143679828 LS-SNP   dbSNP   A 365 C - > F Helix 0% (Buried) 6 86197197
    rs2229523 LS-SNP   dbSNP   A 376 T - > A Turn 45% (Exposed) 6 86199233
    rs2229524 LS-SNP   dbSNP   A 379 M - > KRT 3/10 Helix 70% (Exposed) 6 86199243
    rs144719925 LS-SNP   dbSNP   A 401 R - > C Turn 57% (Exposed) 6 86199308
    rs139549986 LS-SNP   dbSNP   A 401 R - > P Turn 57% (Exposed) 6 86199309
    rs138876213 LS-SNP   dbSNP   A 403 N - > H Turn 92% (Exposed) 6 86199314
    rs146054415 LS-SNP   dbSNP   A 418 G - > E Coil 52% (Exposed) 6 86200268
    rs72905321 LS-SNP   dbSNP   A 421 F - > Y Beta Ladder 5% (Buried) 6 86200277
    rs201008460 LS-SNP   dbSNP   A 463 R - > Q Bend 43% (Exposed) 6 86201722
    rs142656691 LS-SNP   dbSNP   A 470 V - > I Beta Ladder 51% (Exposed) 6 86201742
    rs143859595 LS-SNP   dbSNP   A 491 E - > K Bend 53% (Exposed) 6 86201805
    rs151304292 LS-SNP   dbSNP   A 493 Y - > C Beta Ladder 13% (Intermediate) 6 86201812
    rs145505137 LS-SNP   dbSNP   A 514 E - > D Helix 24% (Intermediate) 6 86201876
    rs141170507 LS-SNP   dbSNP   A 518 H - > Y Beta Ladder 36% (Intermediate) 6 86201886
    rs34160251 LS-SNP   dbSNP   A 530 T - > A Helix 54% (Exposed) 6 86203585