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Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in the closed conformation
Biology and Chemistry Report
1HVY
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text Tomudex, Raltitrexed, TRANSFERASE

    Polymeric Molecules

    Chain A,B,C,D
    Description THYMIDYLATE SYNTHASE 
    Fragment RESIDUES 26-313 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 33112.2 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BME  BETA-MERCAPTOETHANOL  C2 H6 O S   78.13  View 
    D16  TOMUDEX  C21 H22 N4 O6 S   458.49  View 
    UMP  2'-DEOXYURIDINE 5'-MONOPHOSPHATE  C9 H13 N2 O8 P   308.18  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D TYSY_HUMAN P04818     

    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 B C D  2.1.1.45        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    9165   Nucleotide Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation 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). 
    32259   Methylation  The Process in Which a Methyl Group Is Covalently Attached to a 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. 
    5743   Mitochondrial Inner Membrane  The Inner I.e. Lumen Facing Lipid Bilayer of the Mitochondrial Envelope. It Is Highly Folded to Form Cristae. 
    5759   Mitochondrial Matrix  The Gel Like Material with Considerable Fine Structure That Lies in the Matrix Space or Lumen of a Mitochondrion. It Contains the Enzymes of the Tricarboxylic Acid Cycle and in Some Organisms the Enzymes Concerned with Fatty Acid Oxidation. 
    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. 
    8168   Methyltransferase Activity  Catalysis of the Transfer of a Methyl Group to an Acceptor 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. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Tx61


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    18 18p11.32 7298     thymidylate synthetase TYMS    

    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
    rs139713318 LS-SNP   dbSNP   A 78 R - > C Turn 50% (Exposed) 18 659667
    rs59755869 LS-SNP   dbSNP   A 100 E - > Q Helix 36% (Intermediate) 18 662164
    rs11540152 LS-SNP   dbSNP   A 117 F - > L Helix 22% (Intermediate) 18 662215
    rs201415512 LS-SNP   dbSNP   A 134 V - > D Coil 8% (Buried) 18 662267
    rs200442141 LS-SNP   dbSNP   A 147 R - > K Coil 52% (Exposed) 18 662306
    rs141666868 LS-SNP   dbSNP   A 148 D - > E Coil 39% (Exposed) 18 662310
    rs596909 LS-SNP   dbSNP   A 157 G - > V Bend 51% (Exposed) 18 669087
    rs11540153 LS-SNP   dbSNP   A 167 T - > I Helix 28% (Intermediate) 18 669117 BME
    rs147052596 LS-SNP   dbSNP   A 170 T - > S Helix 79% (Exposed) 18 669126
    rs201232749 LS-SNP   dbSNP   A 216 S - > L Beta Ladder 6% (Buried) 18 670782 UMP