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BioLiP
Download all results in tab-seperated text for 3 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 4wzd:6E
    (3.1)    		 BS02 >4wzd:3K (identical to 6n1d:BATN, 4v8d:AB, 4v8d:AD, 4v8d:CB, 4v8d:CD, 4v8e:BB, 4v8e:BD, 4v8e:DB, 4v8e:DD, 4v8f:BB, 4v8f:BD, 4v8f:CB, 4v8f:CD, 4wq1:1K, 4wr6:1K, 4wr6:3K, 4wr6:3L, 4wra:1K, 4wra:3K, 4wra:3L, 4wu1:3K, 4wu1:3L, 4wzd:3L)
    ggugggguucccgagcggccaaagggagcagacuguaaaucugccgucau
cgacuucgaagguucgaauccuucccccaccacca
<<<<<<<..<<<...........>>>.<<<<<.......>>>>>.<<<..
.>>>...<<<<<.......>>>>>>>>>>>>....
    		 ? GO:0000028 ... P17291 26037619
    2 4wzd:71
    (3.1)    		 BS01 >4wzd:3K (identical to 6n1d:BATN, 4v8d:AB, 4v8d:AD, 4v8d:CB, 4v8d:CD, 4v8e:BB, 4v8e:BD, 4v8e:DB, 4v8e:DD, 4v8f:BB, 4v8f:BD, 4v8f:CB, 4v8f:CD, 4wq1:1K, 4wr6:1K, 4wr6:3K, 4wr6:3L, 4wra:1K, 4wra:3K, 4wra:3L, 4wu1:3K, 4wu1:3L, 4wzd:3L)
    ggugggguucccgagcggccaaagggagcagacuguaaaucugccgucau
cgacuucgaagguucgaauccuucccccaccacca
<<<<<<<..<<<...........>>>.<<<<<.......>>>>>.<<<..
.>>>...<<<<<.......>>>>>>>>>>>>....
    		 ? GO:0000049 ... P27150 26037619
    3 4wzd:J8
    (3.1)    		 BS01 >4wzd:3K (identical to 6n1d:BATN, 4v8d:AB, 4v8d:AD, 4v8d:CB, 4v8d:CD, 4v8e:BB, 4v8e:BD, 4v8e:DB, 4v8e:DD, 4v8f:BB, 4v8f:BD, 4v8f:CB, 4v8f:CD, 4wq1:1K, 4wr6:1K, 4wr6:3K, 4wr6:3L, 4wra:1K, 4wra:3K, 4wra:3L, 4wu1:3K, 4wu1:3L, 4wzd:3L)
    ggugggguucccgagcggccaaagggagcagacuguaaaucugccgucau
cgacuucgaagguucgaauccuucccccaccacca
<<<<<<<..<<<...........>>>.<<<<<.......>>>>>.<<<..
.>>>...<<<<<.......>>>>>>>>>>>>....
    		 ? GO:0003735 ... P60494 26037619
    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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