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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
    #     		RNA
    sequence         		EC
    number     		GO
    terms     		UniProt PubMed Binding
    affinity
    1 4nl3:A
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    2 4nl3:B
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    3 4nl3:D
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    4 4nl3:G
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    5 4nl3:H
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    6 4nl3:J
    (3.1)    		 BS01 >4nl3:R (identical to 3af6:B, 4alp:E, 5bkl:kk, 5bkl:qq, 5bkn:h, 5bkn:qq, 5bte:D, 5bte:C, 8cbw:1, 2db3:H, 6duq:Y, 6duq:Z, 5elx:B, 8enk:M, 7ewq:B, 3ex7:F, 3ex7:J, 7exa:B, 7f1m:R, 7f1m:S, 3fht:C, 3fht:D, 6g2k:R, 6h25:R, 2hyi:F, 2hyi:L, 3ice:G, 3iem:G, 3iem:I, 2j0q:E, 2j0q:H, 2j0s:E, 6jc3:N, 6m7d:B, 1m8v:O, 1m8v:P, 1m8v:Q, 1m8v:R, 1m8v:S, 1m8v:U, 1ml5:C, 4nl3:Z, 3o8c:C, 3o8r:C, 7ozr:N, 3pew:B, 3pey:B, 7qdy:E, 7qdz:E, 5sup:D, 5sup:E, 5sup:F, 3vaf:P, 3vaf:E, 3val:E, 4y91:N, 4y91:O, 7ypw:R, 7yr8:R, 5z9w:R, 7znj:E, 7znj:e, 7znj:J, 7znj:j, 7znj:O, 7znj:o)
    uuuuuu
......
    		 ? GO:0003723 ... Q92C58 25150227 PDBbind: Kd=3.4uM
    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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