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BioLiP
Download all results in tab-seperated text for 1 receptor-ligand interactions, whose format is explained at readme.txt.
  • Hover over PDB to view the title of the structure. Click PDB to view the structure at the RCSB PDB database. Resolution -1.00 means the resolution is unavailable, e.g., for NMR structures.
  • Click Site # to view the binding site structure. Hover over Site # to view the binding residues.
  • The sequence is converted from residues with experimentally determined coordinates in the structure; residues not observed in the 3D structure are excluded.
  • Hover over EC number to view the full name of enzymatic activity.
  • Hover over GO terms to view all GO terms.
  • Hover over UniProt to view the protein name.
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    # PDB
    (resolution)
    Site
    #
    RNA
    sequence
    EC
    number
    GO
    terms
    UniProt PubMed Binding
    affinity
    1 4oq9:I
    (1.45)
    BS04 >4oq9:2 (identical to 6a4e:B, 6a4e:D, 3af6:C, 6d30:C, 1ddl:E, 3er9:D, 4ht9:E, 3ie1:G, 3iem:M, 3iem:O, 3iem:P, 6j7z:C, 5kal:Y, 5kal:Z, 7m2t:t, 7m2t:u, 7m2t:v, 7m2t:w, 7m2t:x, 7m2t:y, 7m2t:z, 7m2t:1, 7m2t:2, 7m2t:3, 7m2t:4, 7m2t:5, 7m2t:6, 7m2t:8, 7m2t:ww, 7m2t:xx, 7m2t:yy, 7m2t:zz, 7m57:t, 7m57:u, 7m57:v, 7m57:x, 7m57:y, 7m57:z, 7m57:1, 7m57:2, 7m57:3, 7m57:4, 7m57:5, 7m57:6, 7m57:8, 7m57:ww, 7m57:xx, 7m57:yy, 5new:C, 4nia:t, 4nia:u, 4nia:v, 4nia:w, 4nia:x, 4nia:y, 4nia:z, 4nia:1, 4nia:2, 4nia:3, 4nia:4, 4nia:5, 4nia:6, 4nia:7, 4nia:8, 4oq8:D, 4oq9:t, 4oq9:u, 4oq9:v, 4oq9:w, 4oq9:x, 4oq9:y, 4oq9:z, 4oq9:1, 4oq9:3, 4oq9:4, 4oq9:5, 4oq9:6, 4oq9:7, 4oq9:8, 2vrt:E, 2vrt:F)
    uu
    ..
    ? GO:0005198 ... P17574 25195746

    Reference:
  • Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang. BioLiP2: an updated structure database for biologically relevent ligand-protein interactions, Nucleic Acids Research, gkad630 (2023).
  • Jianyi Yang, Ambrish Roy, and Yang Zhang. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file).
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