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Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D
Biology and Chemistry Report
3IKQ
  •   Structure Details   Hide

    Structure Keywords

    Keywords SUGAR BINDING PROTEIN
    Text Trimeric recombinant fragment, neck+CRD, Collagen, Disulfide bond, Extracellular matrix, Gaseous exchange, Glycoprotein, Hydroxylation, Lectin, Secreted, Surface film, SUGAR BINDING PROTEIN

    Polymeric Molecules

    Chain A,B,C
    Description Pulmonary surfactant-associated protein D 
    Fragment UNP residues 199-375 
    Mutation P180S 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18835.1 
    Source Method genetically manipulated  
    Entity Name SP-D, PSP-D, Lung surfactant protein D 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    MAN  ALPHA-D-MANNOSE  C6 H12 O6   180.16  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C SFTPD_HUMAN P35247     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C
    GO ID   Ontology GO Term Definition
    30246   Carbohydrate Binding  Interacting Selectively and Non Covalently with Any Carbohydrate Which Includes Monosaccharides Oligosaccharides and Polysaccharides As Well As Substances Derived From Monosaccharides by Reduction of the Carbonyl Group (alditols) by Oxidation of One or More Hydroxy Groups to Afford the Corresponding Aldehydes Ketones or Carboxylic Acids or by Replacement of One or More Hydroxy Group(s) by a Hydrogen Atom. Cyclitols Are Generally Not Regarded As Carbohydrates. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene sftpd, pspd, sftp4
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    10 10q22.2-q23.1 6441     surfactant protein D SFTPD    

    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
    rs3088308 LS-SNP   dbSNP   A 270 S - > T Coil 0% (Buried) 10 81697868
    rs3088308 LS-SNP   dbSNP   A 270 S - > T Coil 0% (Buried) 10 81697868
    rs3088308 LS-SNP   dbSNP   A 270 S - > T Coil 0% (Buried) 10 81697868
    rs202078508 LS-SNP   dbSNP   A 272 R - > C Coil 35% (Intermediate) 10 81697862
    rs202078508 LS-SNP   dbSNP   A 272 R - > C Coil 35% (Intermediate) 10 81697862
    rs202078508 LS-SNP   dbSNP   A 272 R - > C Coil 35% (Intermediate) 10 81697862
    rs140229014 LS-SNP   dbSNP   A 283 L - > P Helix 3% (Buried) 10 81697828
    rs140229014 LS-SNP   dbSNP   A 283 L - > P Helix 3% (Buried) 10 81697828
    rs140229014 LS-SNP   dbSNP   A 283 L - > P Helix 3% (Buried) 10 81697828
    rs4469829 LS-SNP   dbSNP   A 289 E - > K Coil 47% (Exposed) 10 81697811
    rs4469829 LS-SNP   dbSNP   A 289 E - > K Coil 47% (Exposed) 10 81697811
    rs4469829 LS-SNP   dbSNP   A 289 E - > K Coil 47% (Exposed) 10 81697811
    rs17851983 LS-SNP   dbSNP   A 321 E - > K Coil 24% (Intermediate) 10 81697715 NULL
    rs17851983 LS-SNP   dbSNP   A 321 E - > K Coil 24% (Intermediate) 10 81697715 NULL
    rs17851983 LS-SNP   dbSNP   A 321 E - > K Coil 24% (Intermediate) 10 81697715 NULL
    rs142628179 LS-SNP   dbSNP   A 324 D - > N Coil 23% (Intermediate) 10 81697706 NULL
    rs142628179 LS-SNP   dbSNP   A 324 D - > N Coil 23% (Intermediate) 10 81697706 NULL
    rs142628179 LS-SNP   dbSNP   A 324 D - > N Coil 23% (Intermediate) 10 81697706 NULL
    rs200817673 LS-SNP   dbSNP   A 327 G - > R 3/10 Helix 68% (Exposed) 10 81697697 NULL
    rs200817673 LS-SNP   dbSNP   A 327 G - > R 3/10 Helix 68% (Exposed) 10 81697697 NULL
    rs200817673 LS-SNP   dbSNP   A 327 G - > R 3/10 Helix 68% (Exposed) 10 81697697 NULL