POP-OUT | CLOSE
 
human PKM2 with L-serine and FBP bound.
Biology and Chemistry Report
4B2D
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text TRANSFERASE, TUMOUR, PKM2, GLYCOLYSIS

    Polymeric Molecules

    Chain A,B,C
    Description PYRUVATE KINASE ISOZYMES M1/M2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 59832.4 
    Source Method genetically manipulated  
    Entity Name PYRUVATE KINASE M2, CYTOSOLIC THYROID HORMONE-BINDING PROTEIN CTHBP, OPA-INTERACTING PROTEIN 3, OIP-3, PYRUVATE KINASE 2/3, PYRUVATE KINASE MUSCLE ISOZYME, THYROID HORMONE-BINDING PROTEIN 1, THBP1, TUMOR M2-PK, P58 
    Chain D
    Description PYRUVATE KINASE ISOZYMES M1/M2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 59832.4 
    Source Method genetically manipulated  
    Entity Name PYRUVATE KINASE M2, CYTOSOLIC THYROID HORMONE-BINDING PROTEIN CTHBP, OPA-INTERACTING PROTEIN 3, OIP-3, PYRUVATE KINASE 2/3, PYRUVATE KINASE MUSCLE ISOZYME, THYROID HORMONE-BINDING PROTEIN 1, THBP1, TUMOR M2-PK, P58 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    FBP  BETA-FRUCTOSE-1,6-DIPHOSPHATE  C6 H14 O12 P2   340.12  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    SER  SERINE  C3 H7 N O3   105.09  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C KPYM_HUMAN A6NFK3     
    D KPYM_HUMAN A6NFK3     

    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  2.7.1.40      
    2.7.1.40      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C
    GO ID   Ontology GO Term Definition
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    6006   Glucose Metabolic Process  The Chemical Reactions and Pathways Involving Glucose the Aldohexose Gluco Hexose. D Glucose Is Dextrorotatory and Is Sometimes Known As Dextrose; It Is an Important Source of Energy For Living Organisms and Is Found Free As Well As Combined in Homo and Hetero Oligosaccharides and Polysaccharides. 
    6096   Glycolytic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Carbohydrate Into Pyruvate with the Concomitant Production of a Small Amount of Atp. Glycolysis Begins with the Metabolism of a Carbohydrate to Generate Products That Can Enter the Pathway and Ends with the Production of Pyruvate. Pyruvate May Be Converted to Ethanol Lactate or Other Small Molecules or Fed Into the Tca Cycle. 
    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. 
    12501   Programmed Cell Death  A Process Which Begins When a Cell Receives an Internal or External Signal and Activates a Series of Biochemical Events (signaling Pathway). the Process Ends with the Death of the Cell. 
    16310   Phosphorylation  The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    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. 
    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. 
    5929   Cilium  A Specialized Eukaryotic Organelle That Consists of a Filiform Extrusion of the Cell Surface and of Some Cytoplasmic Parts. Each Cilium Is Largely Bounded by an Extrusion of the Cytoplasmic (plasma) Membrane and Contains a Regular Longitudinal Array of Microtubules Anchored to a Basal Body. 
    31012   Extracellular Matrix  A Structure Lying External to One or More Cells Which Provides Structural Support For Cells or Tissues; May Be Completely External to the Cell (as in Animals and Bacteria) or Be Part of the Cell (as in Plants). 
    31982   Vesicle  Any Small Fluid Filled Spherical Organelle Enclosed by Membrane or Protein. 
    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. 
    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. 
    287   Magnesium Ion Binding  Interacting Selectively and Non Covalently with Magnesium (mg) Ions. 
    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. 
    4743   Pyruvate Kinase Activity  Catalysis of the Reaction: ATP + Pyruvate = Adp + Phosphoenolpyruvate. 
    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. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    23026   Mhc Class Ii Protein Complex Binding  Interacting Selectively and Non Covalently with the Class Ii Major Histocompatibility Complex. 
    30955   Potassium Ion Binding  Interacting Selectively and Non Covalently with Potassium (k+) Ions. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain D
    GO ID   Ontology GO Term Definition
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    6006   Glucose Metabolic Process  The Chemical Reactions and Pathways Involving Glucose the Aldohexose Gluco Hexose. D Glucose Is Dextrorotatory and Is Sometimes Known As Dextrose; It Is an Important Source of Energy For Living Organisms and Is Found Free As Well As Combined in Homo and Hetero Oligosaccharides and Polysaccharides. 
    6096   Glycolytic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Carbohydrate Into Pyruvate with the Concomitant Production of a Small Amount of Atp. Glycolysis Begins with the Metabolism of a Carbohydrate to Generate Products That Can Enter the Pathway and Ends with the Production of Pyruvate. Pyruvate May Be Converted to Ethanol Lactate or Other Small Molecules or Fed Into the Tca Cycle. 
    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. 
    12501   Programmed Cell Death  A Process Which Begins When a Cell Receives an Internal or External Signal and Activates a Series of Biochemical Events (signaling Pathway). the Process Ends with the Death of the Cell. 
    16310   Phosphorylation  The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    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. 
    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. 
    5929   Cilium  A Specialized Eukaryotic Organelle That Consists of a Filiform Extrusion of the Cell Surface and of Some Cytoplasmic Parts. Each Cilium Is Largely Bounded by an Extrusion of the Cytoplasmic (plasma) Membrane and Contains a Regular Longitudinal Array of Microtubules Anchored to a Basal Body. 
    31012   Extracellular Matrix  A Structure Lying External to One or More Cells Which Provides Structural Support For Cells or Tissues; May Be Completely External to the Cell (as in Animals and Bacteria) or Be Part of the Cell (as in Plants). 
    31982   Vesicle  Any Small Fluid Filled Spherical Organelle Enclosed by Membrane or Protein. 
    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. 
    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. 
    287   Magnesium Ion Binding  Interacting Selectively and Non Covalently with Magnesium (mg) Ions. 
    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. 
    4743   Pyruvate Kinase Activity  Catalysis of the Reaction: ATP + Pyruvate = Adp + Phosphoenolpyruvate. 
    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. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    23026   Mhc Class Ii Protein Complex Binding  Interacting Selectively and Non Covalently with the Class Ii Major Histocompatibility Complex. 
    30955   Potassium Ion Binding  Interacting Selectively and Non Covalently with Potassium (k+) Ions. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain D
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pet28
    Host Vector Type Plasmid


    Chain A,B,C
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pet28
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    15 15q22 5315     pyruvate kinase, muscle PKM    

    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
    rs11558365 LS-SNP   dbSNP   A 16 Q - > H Turn 18% (Intermediate) 15 72511391
    rs11558375 LS-SNP   dbSNP   A 31 C - > F Helix 1% (Buried) 15 72511347
    rs147939689 LS-SNP   dbSNP   A 56 R - > Q Coil 16% (Intermediate) 15 72509829
    rs201533100 LS-SNP   dbSNP   A 58 V - > A Helix 27% (Intermediate) 15 72509823
    rs11558350 LS-SNP   dbSNP   A 71 V - > G Beta Ladder 0% (Buried) 15 72509784
    rs201467423 LS-SNP   dbSNP   A 80 T - > A Coil 61% (Exposed) 15 72509758
    rs142392595 LS-SNP   dbSNP   A 83 Y - > C Helix 30% (Intermediate) 15 72502818
    rs146173648 LS-SNP   dbSNP   A 147 A - > T 3/10 Helix 66% (Exposed) 15 72502140
    rs112954819 LS-SNP   dbSNP   A 149 M - > V Turn 38% (Exposed) 15 72502134
    rs61753428 LS-SNP   dbSNP   A 155 N - > S Turn 62% (Exposed) 15 72502115
    rs11558351 LS-SNP   dbSNP   A 186 K - > N Beta Ladder 54% (Exposed) 15 72502021
    rs200525707 LS-SNP   dbSNP   A 191 D - > N Bend 48% (Exposed) 15 72501227
    rs11558354 LS-SNP   dbSNP   A 200 G - > C Coil 5% (Buried) 15 72501200
    rs141732747 LS-SNP   dbSNP   A 202 S - > F Beta Ladder 51% (Exposed) 15 72501193
    rs17853396 LS-SNP   dbSNP   A 204 G - > V Coil 1% (Buried) 15 72501187
    rs182730190 LS-SNP   dbSNP   A 214 A - > V Bend 20% (Intermediate) 15 72501157
    rs143294717 LS-SNP   dbSNP   A 222 S - > L Coil 21% (Intermediate) 15 72501133
    rs200822996 LS-SNP   dbSNP   A 226 I - > V Helix 41% (Exposed) 15 72501122
    rs149108298 LS-SNP   dbSNP   A 234 E - > K Helix 62% (Exposed) 15 72501098
    rs149152236 LS-SNP   dbSNP   A 235 Q - > L Helix 23% (Intermediate) 15 72501094
    rs145060432 LS-SNP   dbSNP   A 266 K - > R Beta Ladder 24% (Intermediate) 15 72501001
    rs11558364 LS-SNP   dbSNP   A 275 E - > D Helix 38% (Exposed) 15 72500973
    rs147032160 LS-SNP   dbSNP   A 278 R - > Q Helix 64% (Exposed) 15 72500965
    rs11558353 LS-SNP   dbSNP   A 292 V - > L Beta Ladder 0% (Buried) 15 72499581
    rs11558370 LS-SNP   dbSNP   A 310 Q - > P Helix 1% (Buried) 15 72499526
    rs147956260 LS-SNP   dbSNP   A 316 R - > W Helix 18% (Intermediate) 15 72499509
    rs149836418 LS-SNP   dbSNP   A 318 N - > S Helix 6% (Buried) 15 72499502
    rs2959910 LS-SNP   dbSNP   A 339 R - > P Bend 50% (Exposed) 15 72499193
    rs151078084 LS-SNP   dbSNP   A 378 Q - > E Helix 0% (Buried) 15 72499077
    rs200864323 LS-SNP   dbSNP   A 399 R - > H Helix 17% (Intermediate) 15 72494906
    rs181813553 LS-SNP   dbSNP   A 402 A - > V Bend 12% (Intermediate) 15 72494897
    rs148035865 LS-SNP   dbSNP   A 408 P - > L Helix 35% (Intermediate) 15 72494879
    rs139159354 LS-SNP   dbSNP   A 436 R - > T Helix 58% (Exposed) 15 72494795 FBP
    rs59430203 LS-SNP   dbSNP   A 437 S - > Y Helix 8% (Buried) 15 72492994 FBP
    rs141505399 LS-SNP   dbSNP   A 461 R - > H Helix 18% (Intermediate) 15 72492922
    rs200103010 LS-SNP   dbSNP   A 489 R - > Q Helix 10% (Intermediate) 15 72492838 FBP
    rs11558358 LS-SNP   dbSNP   A 490 V - > L Helix 8% (Buried) 15 72492836