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The structure of a platelet derived growth factor receptor complex
Biology and Chemistry Report
3MJG
  •   Structure Details   Hide

    Structure Keywords

    Keywords Hormone/Transferase
    Text protein-protein complex, growth factor-receptor complex, Transferase-Hormone complex, Hormone-Transferase complex

    Polymeric Molecules

    Chain A,B
    Description Platelet-derived growth factor subunit B 
    Fragment UNP residues 21-185 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19596.4 
    Source Method genetically manipulated  
    Entity Name PDGF subunit B, Platelet-derived growth factor B chain, Platelet-derived growth factor beta polypeptide, PDGF-2, Proto-oncogene c-Sis 
    Chain X,Y
    Description Beta-type platelet-derived growth factor receptor 
    Fragment UNP residues 33-314 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 32493.6 
    Source Method genetically manipulated  
    Entity Name PDGF-R-beta, CD140 antigen-like family member B 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    NDG  2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PDGFB_HUMAN G3XAG8     
    X,Y PGFRB_HUMAN P09619     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    X Y  2.7.10.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    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. 
    8083   Growth Factor Activity  The Function That Stimulates a Cell to Grow or Proliferate. Most Growth Factors Have Other Actions Besides the Induction of Cell Growth or Proliferation. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain X,Y
    Common Name Human
    Scientific Name Homo sapiens  
    Gene pdgfrb
    Host Scientific Name Human  
    Host Cell Line Embryonic Kidney 293 Cells


    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene pdgf2, pdgfb, sis
    Host Scientific Name Human  
    Host Cell Line Embryonic Kidney 293 Cells


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q33.1 5159     platelet-derived growth factor receptor, beta polypeptide PDGFRB    
    22 22q13.1 5155     platelet-derived growth factor beta polypeptide PDGFB    

    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
    rs17565 LS-SNP   dbSNP   A 7 I - > V Coil 76% (Exposed) 22 39627821
    rs141576265 LS-SNP   dbSNP   A 15 E - > K Coil 24% (Intermediate) 22 39627797
    rs139127455 LS-SNP   dbSNP   A 18 T - > M Beta Ladder 28% (Intermediate) 22 39627787
    rs116555717 LS-SNP   dbSNP   A 64 Q - > R Beta Ladder 50% (Exposed) 22 39627649
    rs201990837 LS-SNP   dbSNP   A 76 E - > K Beta Ladder 20% (Intermediate) 22 39626221
    rs200484202 LS-SNP   dbSNP   A 83 I - > V Beta Ladder 41% (Exposed) 22 39626200
    rs143980537 LS-SNP   dbSNP   A 88 T - > M Beta Ladder 70% (Exposed) 22 39626184
    rs147952898 LS-SNP   dbSNP   X 55 S - > L Beta Ladder 20% (Intermediate) 5 149515318
    rs202213873 LS-SNP   dbSNP   X 59 P - > L Coil 40% (Exposed) 5 149515306 NAG
    rs144954868 LS-SNP   dbSNP   X 59 P - > S Coil 40% (Exposed) 5 149515307 NAG
    rs80162387 LS-SNP   dbSNP   X 84 V - > M Beta Ladder 27% (Intermediate) 5 149515232
    rs147303614 LS-SNP   dbSNP   X 88 T - > I Coil 66% (Exposed) 5 149515219
    rs141870925 LS-SNP   dbSNP   X 92 G - > W 3/10 Helix 0% (Buried) 5 149515208
    rs144757799 LS-SNP   dbSNP   X 111 D - > G Coil 99% (Exposed) 5 149515150
    rs149347871 LS-SNP   dbSNP   X 114 K - > N Beta Ladder 41% (Exposed) 5 149515140
    rs138830253 LS-SNP   dbSNP   X 140 T - > M Bend 20% (Intermediate) 5 149514525
    rs144857517 LS-SNP   dbSNP   X 167 V - > I Bend 82% (Exposed) 5 149514445
    rs142683442 LS-SNP   dbSNP   X 177 R - > C Turn 45% (Exposed) 5 149514415
    rs17853027 LS-SNP   dbSNP   X 180 S - > F Beta Ladder 23% (Intermediate) 5 149514405
    rs2229560 LS-SNP   dbSNP   X 194 I - > T Beta Ladder 14% (Intermediate) 5 149514363
    rs145459651 LS-SNP   dbSNP   X 196 D - > Y Turn 93% (Exposed) 5 149514358
    rs116642123 LS-SNP   dbSNP   X 197 R - > K Beta Ladder 82% (Exposed) 5 149514354
    rs147568171 LS-SNP   dbSNP   X 256 R - > W Coil 75% (Exposed) 5 149513317
    rs202093144 LS-SNP   dbSNP   X 262 T - > S Beta Ladder 1% (Buried) 5 149513299
    rs34586048 LS-SNP   dbSNP   X 282 E - > K Coil 51% (Exposed) 5 149513239
    rs147707126 LS-SNP   dbSNP   X 290 T - > S Beta Ladder 12% (Intermediate) 5 149513214
    rs61732347 LS-SNP   dbSNP   X 294 T - > P Beta Ladder 28% (Intermediate) 5 149513203 NAG