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BioLiP
Download all results in tab-seperated text for 8 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 5dnm:A
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P84233 28358030
    2 5dnm:B
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P62799 28358030
    3 5dnm:C
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P06897 28358030
    4 5dnm:D
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P02281 28358030
    5 5dnm:E
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P84233 28358030
    6 5dnm:F
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P62799 28358030
    7 5dnm:G
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P06897 28358030
    8 5dnm:H
    (2.81)    		 BS01 >5dnm:I (identical to 5cp6:I, 5dnn:I, 6ipu:I, 6iq4:I, 4j8u:I, 4j8v:I, 4j8w:I, 4j8x:I, 6k1j:I, 4kgc:I, 3kuy:I, 3mnn:I, 2nzd:I, 8q36:III, 8q3e:III, 8q3m:III, 8q3x:III, 3reh:I, 3rei:I, 4wu8:I, 4wu9:I, 5xf3:I, 5xf4:I, 5xf5:I, 5xf6:I, 4xuj:I)
    atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctcc
atcaaaaggcatgttcagctgaatcagctgaacatgccttttgatggagc
agtttccaaatacacttttggtagtatctgcaggtggatattgat
    		 ? GO:0000786 ... P02281 28358030
    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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