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●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP
Download all results in tab-seperated text for 45686 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.
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  • 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
    701 1gdt:B
    (3.0)    		 BS02 >1gdt:D (identical to 1gdt:F, 2gm4:Y, 1zr2:Y, 1zr2:K, 1zr4:Y, 1zr4:K, 1zr4:V, 1zr4:N)
    ttatcggacactg
    		 ? GO:0000150 ... P03012 7628011
    702 1gdt:B
    (3.0)    		 BS03 >1gdt:E
    cagtgtccgataatttataaa
    		 ? GO:0000150 ... P03012 7628011
    703 1gji:A
    (2.85)    		 BS01 >1gji:C
    gggtttaaagaaattccaga
    		 ? GO:0003677 ... P16236 11587641 PDBbind: Kd=25nM
    704 1gji:A
    (2.85)    		 BS02 >1gji:D
    tctggaatttctttaaaccc
    		 ? GO:0003677 ... P16236 11587641 PDBbind: Kd=25nM
    705 1gji:B
    (2.85)    		 BS01 >1gji:C
    gggtttaaagaaattccaga
    		 ? GO:0003677 ... P16236 11587641 PDBbind: Kd=25nM
    706 1gji:B
    (2.85)    		 BS02 >1gji:D
    tctggaatttctttaaaccc
    		 ? GO:0003677 ... P16236 11587641 PDBbind: Kd=25nM
    707 1glu:A
    (2.9)    		 BS01 >1glu:C (identical to 1glu:D, 1r4o:C, 1r4o:D)
    ccagaacatcgatgttctg
    		 ? GO:0003700 ... P06536 1865905
    708 1glu:A
    (2.9)    		 BS02 >1glu:D (identical to 1glu:C, 1r4o:C, 1r4o:D)
    ccagaacatcgatgttctg
    		 ? GO:0003700 ... P06536 1865905
    709 1glu:B
    (2.9)    		 BS01 >1glu:C (identical to 1glu:D, 1r4o:C, 1r4o:D)
    ccagaacatcgatgttctg
    		 ? GO:0003700 ... P06536 1865905
    710 1glu:B
    (2.9)    		 BS02 >1glu:D (identical to 1glu:C, 1r4o:C, 1r4o:D)
    ccagaacatcgatgttctg
    		 ? GO:0003700 ... P06536 1865905
    711 1gm5:A
    (3.24)    		 BS01 >1gm5:X
    cagctccatgat
    		 3.6.4.12 GO:0003676 ... Q9WY48 11595187
    712 1gm5:A
    (3.24)    		 BS02 >1gm5:Y
    gcagtgctcgcatggagctg
    		 3.6.4.12 GO:0003676 ... Q9WY48 11595187
    713 1gm5:A
    (3.24)    		 BS03 >1gm5:Z (identical to 5n8r:C, 5n8r:D)
    gagcactgc
    		 3.6.4.12 GO:0003676 ... Q9WY48 11595187
    714 1gt0:C
    (2.6)    		 BS01 >1gt0:A
    ttctttgtttggatgctaatggga
    		 ? GO:0000981 ... P14859 12923055
    715 1gt0:C
    (2.6)    		 BS02 >1gt0:B
    atcccattagcatccaaacaaaga
    		 ? GO:0000981 ... P14859 12923055
    716 1gt0:D
    (2.6)    		 BS01 >1gt0:A
    ttctttgtttggatgctaatggga
    		 ? N/A P48432 12923055
    717 1gt0:D
    (2.6)    		 BS02 >1gt0:B
    atcccattagcatccaaacaaaga
    		 ? N/A P48432 12923055
    718 1gtw:A
    (1.85)    		 BS01 >1gtw:C
    aatgtggcgcaatcct
    		 ? GO:0003700 ... P17676 N/A
    719 1gtw:A
    (1.85)    		 BS02 >1gtw:D
    taggattgcgccacat
    		 ? GO:0003700 ... P17676 N/A
    720 1gtw:B
    (1.85)    		 BS01 >1gtw:C
    aatgtggcgcaatcct
    		 ? GO:0003700 ... P17676 N/A
    721 1gtw:B
    (1.85)    		 BS02 >1gtw:D
    taggattgcgccacat
    		 ? GO:0003700 ... P17676 N/A
    722 1gu4:A
    (1.8)    		 BS01 >1gu4:C (identical to 2e42:C, 2e43:C)
    taggattgcgcaatat
    		 ? GO:0003700 ... P17676 N/A
    723 1gu4:A
    (1.8)    		 BS02 >1gu4:D (identical to 2e42:D, 2e43:D)
    aatattgcgcaatcct
    		 ? GO:0003700 ... P17676 N/A
    724 1gu4:B
    (1.8)    		 BS01 >1gu4:C (identical to 2e42:C, 2e43:C)
    taggattgcgcaatat
    		 ? GO:0003700 ... P17676 N/A
    725 1gu4:B
    (1.8)    		 BS02 >1gu4:D (identical to 2e42:D, 2e43:D)
    aatattgcgcaatcct
    		 ? GO:0003700 ... P17676 N/A
    726 1gu5:A
    (2.1)    		 BS01 >1gu5:C
    ttgtgttggccaatca
    		 ? GO:0003700 ... P17676 N/A
    727 1gu5:A
    (2.1)    		 BS02 >1gu5:D
    atgattggccaacaca
    		 ? GO:0003700 ... P17676 N/A
    728 1gu5:B
    (2.1)    		 BS01 >1gu5:C
    ttgtgttggccaatca
    		 ? GO:0003700 ... P17676 N/A
    729 1gu5:B
    (2.1)    		 BS02 >1gu5:D
    atgattggccaacaca
    		 ? GO:0003700 ... P17676 N/A
    730 1gxp:A
    (2.5)    		 BS01 >1gxp:C (identical to 1gxp:G)
    gagctgtcataaagttgtcacgg
    		 ? GO:0000160 ... P0AFJ5 12015152
    731 1gxp:A
    (2.5)    		 BS02 >1gxp:D (identical to 1gxp:H)
    cccgtgacaactttatgacagct
    		 ? GO:0000160 ... P0AFJ5 12015152
    732 1gxp:B
    (2.5)    		 BS01 >1gxp:C (identical to 1gxp:G)
    gagctgtcataaagttgtcacgg
    		 ? GO:0000160 ... P0AFJ5 12015152
    733 1gxp:B
    (2.5)    		 BS02 >1gxp:D (identical to 1gxp:H)
    cccgtgacaactttatgacagct
    		 ? GO:0000160 ... P0AFJ5 12015152
    734 1gxp:E
    (2.5)    		 BS01 >1gxp:G (identical to 1gxp:C)
    gagctgtcataaagttgtcacgg
    		 ? GO:0000160 ... P0AFJ5 12015152
    735 1gxp:E
    (2.5)    		 BS02 >1gxp:H (identical to 1gxp:D)
    cccgtgacaactttatgacagct
    		 ? GO:0000160 ... P0AFJ5 12015152
    736 1gxp:F
    (2.5)    		 BS01 >1gxp:G (identical to 1gxp:C)
    gagctgtcataaagttgtcacgg
    		 ? GO:0000160 ... P0AFJ5 12015152
    737 1gxp:F
    (2.5)    		 BS02 >1gxp:H (identical to 1gxp:D)
    cccgtgacaactttatgacagct
    		 ? GO:0000160 ... P0AFJ5 12015152
    738 1h0m:A
    (3.0)    		 BS01 >1h0m:E (identical to 1h0m:F, 1h0m:G, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    739 1h0m:A
    (3.0)    		 BS02 >1h0m:F (identical to 1h0m:E, 1h0m:G, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    740 1h0m:B
    (3.0)    		 BS01 >1h0m:E (identical to 1h0m:F, 1h0m:G, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    741 1h0m:B
    (3.0)    		 BS02 >1h0m:F (identical to 1h0m:E, 1h0m:G, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    742 1h0m:C
    (3.0)    		 BS01 >1h0m:G (identical to 1h0m:E, 1h0m:F, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    743 1h0m:C
    (3.0)    		 BS02 >1h0m:H (identical to 1h0m:E, 1h0m:F, 1h0m:G)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    744 1h0m:D
    (3.0)    		 BS01 >1h0m:G (identical to 1h0m:E, 1h0m:F, 1h0m:H)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    745 1h0m:D
    (3.0)    		 BS02 >1h0m:H (identical to 1h0m:E, 1h0m:F, 1h0m:G)
    atgtgcagatctgcacat
    		 ? GO:0000976 ... P33905 12198141
    746 1h38:A
    (2.9)    		 BS01 >1h38:E (identical to 8dh1:F, 8dh2:A, 8dh2:F, 8dh3:F, 8dh3:N, 8dh4:F, 8dh5:F, 8dh5:N, 1h38:K, 1h38:N)
    ggaatcgacatcgccgc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    747 1h38:A
    (2.9)    		 BS03 >1h38:G (identical to 1h38:P, 1s0v:G, 1s0v:P)
    gtcgattcc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    748 1h38:B
    (2.9)    		 BS01 >1h38:H
    gggaatcgacatcgccgc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    749 1h38:C
    (2.9)    		 BS01 >1h38:K (identical to 8dh1:F, 8dh2:A, 8dh2:F, 8dh3:F, 8dh3:N, 8dh4:F, 8dh5:F, 8dh5:N, 1h38:E, 1h38:N)
    ggaatcgacatcgccgc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    750 1h38:D
    (2.9)    		 BS01 >1h38:N (identical to 8dh1:F, 8dh2:A, 8dh2:F, 8dh3:F, 8dh3:N, 8dh4:F, 8dh5:F, 8dh5:N, 1h38:E, 1h38:K)
    ggaatcgacatcgccgc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    751 1h38:D
    (2.9)    		 BS03 >1h38:P (identical to 1h38:G, 1s0v:G, 1s0v:P)
    gtcgattcc
    		 2.7.7.6 GO:0000428 ... P00573 12422209
    752 1h6f:A
    (1.7)    		 BS01 >1h6f:C (identical to 1h6f:D)
    taatttcacacctaggtgtgaaat
    		 ? GO:0000978 ... O15119 12005433
    753 1h6f:A
    (1.7)    		 BS02 >1h6f:D (identical to 1h6f:C)
    taatttcacacctaggtgtgaaat
    		 ? GO:0000978 ... O15119 12005433
    754 1h6f:B
    (1.7)    		 BS01 >1h6f:C (identical to 1h6f:D)
    taatttcacacctaggtgtgaaat
    		 ? GO:0000978 ... O15119 12005433
    755 1h6f:B
    (1.7)    		 BS02 >1h6f:D (identical to 1h6f:C)
    taatttcacacctaggtgtgaaat
    		 ? GO:0000978 ... O15119 12005433
    756 1h88:A
    (2.8)    		 BS01 >1h88:D (identical to 1h89:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=35.3nM
    757 1h88:A
    (2.8)    		 BS02 >1h88:E (identical to 1h89:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=35.3nM
    758 1h88:B
    (2.8)    		 BS01 >1h88:D (identical to 1h89:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=35.3nM
    759 1h88:B
    (2.8)    		 BS02 >1h88:E (identical to 1h89:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=35.3nM
    760 1h88:C
    (2.8)    		 BS01 >1h88:D (identical to 1h89:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? N/A P06876 11792321 PDBbind: Kd=35.3nM
    761 1h88:C
    (2.8)    		 BS02 >1h88:E (identical to 1h89:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? N/A P06876 11792321 PDBbind: Kd=35.3nM
    762 1h89:A
    (2.45)    		 BS01 >1h89:D (identical to 1h88:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=1.64nM
    763 1h89:A
    (2.45)    		 BS02 >1h89:E (identical to 1h88:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=1.64nM
    764 1h89:B
    (2.45)    		 BS01 >1h89:D (identical to 1h88:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=1.64nM
    765 1h89:B
    (2.45)    		 BS02 >1h89:E (identical to 1h88:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=1.64nM
    766 1h89:C
    (2.45)    		 BS01 >1h89:D (identical to 1h88:D, 1h8a:D)
    gatgtggcgcaatccttaacggactg
    		 ? N/A P06876 11792321 PDBbind: Kd=1.64nM
    767 1h89:C
    (2.45)    		 BS02 >1h89:E (identical to 1h88:E, 1h8a:E)
    ccagtccgttaaggattgcgccacat
    		 ? N/A P06876 11792321 PDBbind: Kd=1.64nM
    768 1h8a:A
    (2.23)    		 BS01 >1h8a:D (identical to 1h88:D, 1h89:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=25.4nM
    769 1h8a:A
    (2.23)    		 BS02 >1h8a:E (identical to 1h88:E, 1h89:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=25.4nM
    770 1h8a:B
    (2.23)    		 BS01 >1h8a:D (identical to 1h88:D, 1h89:D)
    gatgtggcgcaatccttaacggactg
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=25.4nM
    771 1h8a:B
    (2.23)    		 BS02 >1h8a:E (identical to 1h88:E, 1h89:E)
    ccagtccgttaaggattgcgccacat
    		 ? GO:0003700 ... P17676 11792321 PDBbind: Kd=25.4nM
    772 1h8a:C
    (2.23)    		 BS01 >1h8a:D (identical to 1h88:D, 1h89:D)
    gatgtggcgcaatccttaacggactg
    		 ? N/A P01104 11792321 PDBbind: Kd=25.4nM
    773 1h8a:C
    (2.23)    		 BS02 >1h8a:E (identical to 1h88:E, 1h89:E)
    ccagtccgttaaggattgcgccacat
    		 ? N/A P01104 11792321 PDBbind: Kd=25.4nM
    774 1h9d:A
    (2.6)    		 BS01 >1h9d:E (identical to 1h9d:G)
    gttgcggttg
    		 ? GO:0003677 ... Q01196 11276260 PDBbind: Kd=10pM
    775 1h9d:A
    (2.6)    		 BS02 >1h9d:F (identical to 1h9d:H)
    caaccgcaac
    		 ? GO:0003677 ... Q01196 11276260 PDBbind: Kd=10pM
    776 1h9d:C
    (2.6)    		 BS01 >1h9d:G (identical to 1h9d:E)
    gttgcggttg
    		 ? GO:0003677 ... Q01196 11276260 PDBbind: Kd=10pM
    777 1h9d:C
    (2.6)    		 BS02 >1h9d:H (identical to 1h9d:F)
    caaccgcaac
    		 ? GO:0003677 ... Q01196 11276260 PDBbind: Kd=10pM
    778 1h9t:A
    (3.25)    		 BS01 >1h9t:X
    catctggtacgaccagatc
    		 ? GO:0000062 ... P0A8V6 11296236 PDBbind: Kd=0.2nM
    779 1h9t:A
    (3.25)    		 BS02 >1h9t:Y
    gatctggtcgtaccagatg
    		 ? GO:0000062 ... P0A8V6 11296236 PDBbind: Kd=0.2nM
    780 1h9t:B
    (3.25)    		 BS01 >1h9t:X
    catctggtacgaccagatc
    		 ? GO:0000062 ... P0A8V6 11296236 PDBbind: Kd=0.2nM
    781 1h9t:B
    (3.25)    		 BS02 >1h9t:Y
    gatctggtcgtaccagatg
    		 ? GO:0000062 ... P0A8V6 11296236 PDBbind: Kd=0.2nM
    782 1hao:H
    (2.8)    		 BS01 >1hao:D (identical to 4dih:D, 4dii:D, 6eo6:D, 6eo7:D, 1hap:D, 1hut:D, 3qlp:D, 6z8v:A, 6z8w:A, 7zkl:A, 7zkm:B, 7zkn:E)
    ggttggtgtggttgg
    		 3.4.21.5 GO:0004252 ... P00734 15299700
    783 1hap:H
    (2.8)    		 BS01 >1hap:D (identical to 4dih:D, 4dii:D, 6eo6:D, 6eo7:D, 1hao:D, 1hut:D, 3qlp:D, 6z8v:A, 6z8w:A, 7zkl:A, 7zkm:B, 7zkn:E)
    ggttggtgtggttgg
    		 3.4.21.5 GO:0004252 ... P00734 15299700
    784 1hbx:A
    (3.15)    		 BS01 >1hbx:C (identical to 1hbx:F)
    gatggcctaattaggacttccggtgt
    		 ? GO:0000981 ... P11831 11406578
    785 1hbx:A
    (3.15)    		 BS02 >1hbx:W (identical to 1hbx:X)
    cacaccggaagtcctaattaggccat
    		 ? GO:0000981 ... P11831 11406578
    786 1hbx:B
    (3.15)    		 BS01 >1hbx:C (identical to 1hbx:F)
    gatggcctaattaggacttccggtgt
    		 ? GO:0000981 ... P11831 11406578
    787 1hbx:B
    (3.15)    		 BS02 >1hbx:W (identical to 1hbx:X)
    cacaccggaagtcctaattaggccat
    		 ? GO:0000981 ... P11831 11406578
    788 1hbx:D
    (3.15)    		 BS01 >1hbx:F (identical to 1hbx:C)
    gatggcctaattaggacttccggtgt
    		 ? GO:0000981 ... P11831 11406578
    789 1hbx:D
    (3.15)    		 BS02 >1hbx:X (identical to 1hbx:W)
    cacaccggaagtcctaattaggccat
    		 ? GO:0000981 ... P11831 11406578
    790 1hbx:E
    (3.15)    		 BS01 >1hbx:F (identical to 1hbx:C)
    gatggcctaattaggacttccggtgt
    		 ? GO:0000981 ... P11831 11406578
    791 1hbx:E
    (3.15)    		 BS02 >1hbx:X (identical to 1hbx:W)
    cacaccggaagtcctaattaggccat
    		 ? GO:0000981 ... P11831 11406578
    792 1hbx:G
    (3.15)    		 BS01 >1hbx:C (identical to 1hbx:F)
    gatggcctaattaggacttccggtgt
    		 ? GO:0003700 ... P28324 11406578
    793 1hbx:G
    (3.15)    		 BS02 >1hbx:W (identical to 1hbx:X)
    cacaccggaagtcctaattaggccat
    		 ? GO:0003700 ... P28324 11406578
    794 1hbx:H
    (3.15)    		 BS01 >1hbx:F (identical to 1hbx:C)
    gatggcctaattaggacttccggtgt
    		 ? GO:0003700 ... P28324 11406578
    795 1hbx:H
    (3.15)    		 BS02 >1hbx:X (identical to 1hbx:W)
    cacaccggaagtcctaattaggccat
    		 ? GO:0003700 ... P28324 11406578
    796 1hcq:A
    (2.4)    		 BS01 >1hcq:C (identical to 1hcq:G)
    ccaggtcacagtgacctg
    		 ? GO:0003700 ... P03372 8221895
    797 1hcq:A
    (2.4)    		 BS02 >1hcq:D (identical to 1hcq:H)
    ccaggtcactgtgacctg
    		 ? GO:0003700 ... P03372 8221895
    798 1hcq:B
    (2.4)    		 BS01 >1hcq:C (identical to 1hcq:G)
    ccaggtcacagtgacctg
    		 ? GO:0003700 ... P03372 8221895
    799 1hcq:B
    (2.4)    		 BS02 >1hcq:D (identical to 1hcq:H)
    ccaggtcactgtgacctg
    		 ? GO:0003700 ... P03372 8221895
    800 1hcq:E
    (2.4)    		 BS01 >1hcq:G (identical to 1hcq:C)
    ccaggtcacagtgacctg
    		 ? GO:0003700 ... P03372 8221895
    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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