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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
    #     		DNA
    sequence         		EC
    number     		GO
    terms     		UniProt PubMed Binding
    affinity
    1 4gck:A
    (2.05)    		 BS02 >4gck:Z (identical to 4gck:W, 5haw:Z, 5hbu:W, 5hbu:Z, 5hbu:R, 5hbu:T, 5k58:R, 5k58:T)
    gtgagtactcac
    		 ? GO:0000976 ... B5XTG2 23754405 PDBbind: Kd=162.4nM
    2 4gck:C
    (2.05)    		 BS02 >4gck:Z (identical to 4gck:W, 5haw:Z, 5hbu:W, 5hbu:Z, 5hbu:R, 5hbu:T, 5k58:R, 5k58:T)
    gtgagtactcac
    		 ? GO:0000976 ... B5XTG2 23754405 PDBbind: Kd=162.4nM
    3 4gck:D
    (2.05)    		 BS01 >4gck:Z (identical to 4gck:W, 5haw:Z, 5hbu:W, 5hbu:Z, 5hbu:R, 5hbu:T, 5k58:R, 5k58:T)
    gtgagtactcac
    		 ? GO:0000976 ... B5XTG2 23754405 PDBbind: Kd=162.4nM
    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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