An Information Portal to 105212 Biological Macromolecular Structures

Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, tetragonal crystal form
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords


    Polymeric Molecules

    Chain A,B
    Description GDP-L-FUCOSE SYNTHASE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35872.8 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GDP  GUANOSINE-5'-DIPHOSPHATE  C10 H15 N5 O11 P2   443.20  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B FCL_HUMAN B2R8Y7     

    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: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    7159   Leukocyte Cell Cell Adhesion  The Attachment of a Leukocyte to Another Cell Via Adhesion Molecules. 
    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. 
    19673   GDP Mannose Metabolic Process  The Chemical Reactions and Pathways Involving GDP Mannose a Substance Composed of Mannose in Glycosidic Linkage with Guanosine Diphosphate. 
    19835   Cytolysis  The Rupture of Cell Membranes and the Loss of Cytoplasm. 
    42351   'de Novo' GDP L Fucose Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of GDP L Fucose From GDP D Mannose Via GDP 4 Dehydro 6 Deoxy D Mannose Requiring the Functions of GDP Mannose 4 6 Dehydratase (ec: and GDP L Fucose Synthase (ec: 
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    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. 
    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. 
    9055   Electron Carrier Activity  Any Molecular Entity That Serves As an Electron Acceptor and Electron Donor in an Electron Transport Chain. an Electron Transport Chain Is a Process in Which a Series of Electron Carriers Operate Together to Transfer Electrons From Donors to Any of Several Different Terminal Electron Acceptors to Generate a Transmembrane Electrochemical Gradient. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    16853   Isomerase Activity  Catalysis of the Geometric or Structural Changes Within One Molecule. Isomerase Is the Systematic Name For Any Enzyme of EC Class 5. 
    42356   GDP 4 Dehydro D Rhamnose Reductase Activity  Catalysis of the Reaction: GDP 6 Deoxy D Mannose + Nad(p)+ = GDP 4 Dehydro 6 Deoxy D Mannose + Nad(p)h + H+. in the Reverse Reaction a Mixture of GDP D Rhamnose and Its C 4 Epimer Is Formed. 
    50577   GDP L Fucose Synthase Activity  Catalysis of the Reaction: GDP L Fucose + Nad+ = GDP 4 Dehydro 6 Deoxy D Mannose + Nadh + H+. 
    50662   Coenzyme Binding  Interacting Selectively and Non Covalently with a Coenzyme Any of Various Nonprotein Organic Cofactors That Are Required in Addition to an Enzyme and a Substrate For an Enzymatic Reaction to Proceed. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Variant R3
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PNIC28-BSA4

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    8 8q24.3 7264     tissue specific transplantation antigen P35B TSTA3    

    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
    rs191134608 LS-SNP   dbSNP   A -4 P - > H Coil 46% (Exposed) 8 144698872
    rs140495027 LS-SNP   dbSNP   A 13 K - > R Beta Ladder 1% (Buried) 8 144698821
    rs143598669 LS-SNP   dbSNP   A 38 A - > V Beta Ladder 19% (Intermediate) 8 144698746
    rs139998516 LS-SNP   dbSNP   A 47 R - > C Coil 38% (Exposed) 8 144698374 NAP
    rs113656512 LS-SNP   dbSNP   A 65 V - > G Beta Ladder 25% (Intermediate) 8 144698319
    rs143026820 LS-SNP   dbSNP   A 70 R - > W Coil 13% (Intermediate) 8 144698305 NAP
    rs148674156 LS-SNP   dbSNP   A 72 I - > M Coil 13% (Intermediate) 8 144698297 NAP
    rs149496415 LS-SNP   dbSNP   A 99 R - > H Helix 24% (Intermediate) 8 144697027
    rs201411011 LS-SNP   dbSNP   A 99 R - > C Helix 24% (Intermediate) 8 144697028
    rs199822261 LS-SNP   dbSNP   A 125 N - > S Bend 46% (Exposed) 8 144696860
    rs138619385 LS-SNP   dbSNP   A 129 H - > D 3/10 Helix 65% (Exposed) 8 144696849
    rs150279875 LS-SNP   dbSNP   A 132 N - > S 3/10 Helix 4% (Buried) 8 144696839
    rs201368998 LS-SNP   dbSNP   A 142 I - > V Helix 0% (Buried) 8 144696810
    rs200572513 LS-SNP   dbSNP   A 162 P - > S Coil 55% (Exposed) 8 144696580
    rs201464118 LS-SNP   dbSNP   A 164 N - > S Beta Ladder 31% (Intermediate) 8 144696573
    rs150364101 LS-SNP   dbSNP   A 165 V - > I Beta Ladder 0% (Buried) 8 144696571
    rs140641547 LS-SNP   dbSNP   A 170 D - > N Beta Ladder 4% (Buried) 8 144696556 NAP
    rs145040472 LS-SNP   dbSNP   A 175 E - > K Coil 0% (Buried) 8 144696541
    rs141236351 LS-SNP   dbSNP   A 195 S - > L Helix 0% (Buried) 8 144696389
    rs139620518 LS-SNP   dbSNP   A 198 T - > M Helix 6% (Buried) 8 144696380
    rs201183774 LS-SNP   dbSNP   A 204 N - > D Coil 41% (Exposed) 8 144696363
    rs142621980 LS-SNP   dbSNP   A 205 P - > L Beta Ladder 1% (Buried) 8 144696359
    rs147382289 LS-SNP   dbSNP   A 206 R - > Q Beta Ladder 47% (Exposed) 8 144696356
    rs199878471 LS-SNP   dbSNP   A 312 R - > G Helix 1% (Buried) 8 144695088