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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 8ybj:A
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P68431 38972377
    2 8ybj:B
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000781 ... P62805 38972377
    3 8ybj:C
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P04908 38972377
    4 8ybj:D
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P06899 38972377
    5 8ybj:E
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P68431 38972377
    6 8ybj:F
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000781 ... P62805 38972377
    7 8ybj:G
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P04908 38972377
    8 8ybj:H
    (2.38)    		 BS02 >8ybj:J (identical to 7c0m:J, 7c0m:j, 7d1z:J, 8g6q:J, 8g6s:J, 8jlb:J, 8jld:J, 5kgf:J, 3lz0:J, 3lz1:I, 5mlu:I, 6nn6:J, 8of4:J, 7oh9:J, 7ohb:J, 7ohc:J, 6se0:J, 6se6:J, 6see:J, 6sef:J, 6seg:J, 6t9l:J, 7w9v:J, 7wlr:J, 7yqk:J, 6z6p:J, 6zhx:J, 4zux:J, 4zux:T)
    atcgatgtatatatctgacacgtgcctggagactagggagtaatcccctt
ggcggttaaaacgcgggggacagcgcgtacgtgcgtttaagcggtgctag
agctgtctacgaccaattgagcggcctcggcaccgggattctgat
    		 N/A GO:0000786 ... P06899 38972377
    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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