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BioLiP
Download all results in tab-seperated text for 6 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
    #     		DNA
    sequence         		EC
    number     		GO
    terms     		UniProt PubMed Binding
    affinity
    1 5iyd:A
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 2.7.7.48
    2.7.7.6
    3.1.13.-    		 GO:0000287 ... P24928 27193682
    2 5iyd:B
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 2.7.7.48
    2.7.7.6
    3.1.13.-    		 GO:0000428 ... P30876 27193682
    3 5iyd:E
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 ? GO:0000428 ... P19388 27193682
    4 5iyd:M
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 2.3.1.48 GO:0000776 ... Q00403 27193682
    5 5iyd:P
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 ? GO:0000785 ... P20226 27193682
    6 5iyd:T
    (3.9)    		 BS01 >5iyd:X (identical to 5iyc:X)
    gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctac
    		 3.6.4.12 GO:0003677 ... P13984 27193682
    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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