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I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM DMFold SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

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.
  • 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
    401 1dew:B
    (2.65)
    BS01 >1dew:X (identical to 1dew:U, 2nqj:C)
    gcgtccccgacgacg
    3.1.11.2
    3.1.21.-
    GO:0003677 ... P27695 10667800
    402 1dew:B
    (2.65)
    BS02 >1dew:Y (identical to 1dew:V)
    gtcgtcggggacgc
    3.1.11.2
    3.1.21.-
    GO:0003677 ... P27695 10667800
    403 1dfm:A
    (1.5)
    BS01 >1dfm:C (identical to 1d2i:C, 1d2i:D, 1dfm:D)
    tattatagatctataa
    3.1.21.4 GO:0000287 ... Q45488 10655616
    404 1dfm:A
    (1.5)
    BS02 >1dfm:D (identical to 1d2i:C, 1d2i:D, 1dfm:C)
    tattatagatctataa
    3.1.21.4 GO:0000287 ... Q45488 10655616
    405 1dfm:B
    (1.5)
    BS01 >1dfm:C (identical to 1d2i:C, 1d2i:D, 1dfm:D)
    tattatagatctataa
    3.1.21.4 GO:0000287 ... Q45488 10655616
    406 1dfm:B
    (1.5)
    BS02 >1dfm:D (identical to 1d2i:C, 1d2i:D, 1dfm:C)
    tattatagatctataa
    3.1.21.4 GO:0000287 ... Q45488 10655616
    407 1dgc:A
    (3.0)
    BS01 >1dgc:B (identical to 2dgc:B)
    tggagatgacgtcatctcc
    ? GO:0003700 ... P03069 8377181
    408 1dh3:A
    (3.0)
    BS01 >1dh3:B (identical to 1dh3:D)
    ccttggctgacgtcagccaag
    ? GO:0003677 ... Q01147 10952992 PDBbind: Kd=1.4nM
    409 1dh3:C
    (3.0)
    BS01 >1dh3:D (identical to 1dh3:B)
    ccttggctgacgtcagccaag
    ? GO:0003677 ... Q01147 10952992 PDBbind: Kd=1.4nM
    410 1diz:A
    (2.5)
    BS01 >1diz:E (identical to 1diz:C)
    gacatgactgcct
    3.2.2.21 GO:0003824 ... P04395 10675345
    411 1diz:A
    (2.5)
    BS02 >1diz:F (identical to 1bnk:E, 1diz:D, 1f6o:E)
    ggcaatcatgtca
    3.2.2.21 GO:0003824 ... P04395 10675345
    412 1diz:B
    (2.5)
    BS01 >1diz:C (identical to 1diz:E)
    gacatgactgcct
    3.2.2.21 GO:0003824 ... P04395 10675345
    413 1diz:B
    (2.5)
    BS02 >1diz:D (identical to 1bnk:E, 1diz:F, 1f6o:E)
    ggcaatcatgtca
    3.2.2.21 GO:0003824 ... P04395 10675345
    414 1dmu:A
    (2.2)
    BS01 >1dmu:F
    atcgcctaataggcgat
    3.1.21.4 GO:0004519 ... O68557 9736624
    415 1dnk:A
    (2.3)
    BS01 >1dnk:B
    ggtatac
    3.1.21.1 GO:0002283 ... P00639 1518054
    416 1dnk:A
    (2.3)
    BS02 >1dnk:C
    ggtatacc
    3.1.21.1 GO:0002283 ... P00639 1518054
    417 1dp7:P
    (1.5)
    BS01 >1dp7:D
    cgutaccauggtaacg
    ? GO:0003677 ... P22670 10706293
    418 1drg:A
    (2.55)
    BS01 >1drg:B (identical to 1f44:M)
    tataacttcgtatagc
    ? GO:0003677 ... P06956 11601846
    419 1drg:A
    (2.55)
    BS02 >1drg:C (identical to 1crx:D, 1crx:F, 1f44:N)
    atatgctatacgaagttat
    ? GO:0003677 ... P06956 11601846
    420 1dsz:A
    (1.7)
    BS01 >1dsz:C
    caggtcaaaggtcag
    ? GO:0003700 ... P10276 10698945
    421 1dsz:A
    (1.7)
    BS02 >1dsz:D
    ctgacctttgacctg
    ? GO:0003700 ... P10276 10698945
    422 1dsz:B
    (1.7)
    BS01 >1dsz:C
    caggtcaaaggtcag
    ? GO:0003700 ... P19793 10698945
    423 1dsz:B
    (1.7)
    BS02 >1dsz:D
    ctgacctttgacctg
    ? GO:0003700 ... P19793 10698945
    424 1du0:A
    (2.0)
    BS01 >1du0:C (identical to 1hdd:A, 3hdd:C)
    ttttgccatgtaattacctaa
    ? GO:0000981 ... P02836 10889025 PDBbind: Kd=79pM
    425 1du0:A
    (2.0)
    BS02 >1du0:D (identical to 1hdd:B, 3hdd:D)
    attaggtaattacatggcaaa
    ? GO:0000981 ... P02836 10889025 PDBbind: Kd=79pM
    426 1du0:B
    (2.0)
    BS01 >1du0:C (identical to 1hdd:A, 3hdd:C)
    ttttgccatgtaattacctaa
    ? GO:0000981 ... P02836 10889025 PDBbind: Kd=79pM
    427 1du0:B
    (2.0)
    BS02 >1du0:D (identical to 1hdd:B, 3hdd:D)
    attaggtaattacatggcaaa
    ? GO:0000981 ... P02836 10889025 PDBbind: Kd=79pM
    428 1dux:C
    (2.1)
    BS01 >1dux:A (identical to 1dux:D)
    tgaccggaagtgt
    ? GO:0003700 ... P19419 10742173
    429 1dux:C
    (2.1)
    BS02 >1dux:B (identical to 1dux:E)
    acacttccggtca
    ? GO:0003700 ... P19419 10742173
    430 1dux:F
    (2.1)
    BS01 >1dux:D (identical to 1dux:A)
    tgaccggaagtgt
    ? GO:0003700 ... P19419 10742173
    431 1dux:F
    (2.1)
    BS02 >1dux:E (identical to 1dux:B)
    acacttccggtca
    ? GO:0003700 ... P19419 10742173
    432 1e3m:A
    (2.2)
    BS01 >1e3m:E (identical to 3k0s:E, 1ng9:E, 1oh7:E, 1w7a:E, 1wb9:E, 1wbb:E, 1wbd:E)
    agctgccaggcaccagtg
    ? GO:0000018 ... P23909 11048711
    433 1e3m:A
    (2.2)
    BS02 >1e3m:F (identical to 3k0s:F, 1ng9:F, 1w7a:F, 1wb9:F, 1wbb:F, 1wbd:F, 3zlj:F)
    actggtgcttggcagct
    ? GO:0000018 ... P23909 11048711
    434 1e3m:B
    (2.2)
    BS01 >1e3m:E (identical to 3k0s:E, 1ng9:E, 1oh7:E, 1w7a:E, 1wb9:E, 1wbb:E, 1wbd:E)
    agctgccaggcaccagtg
    ? GO:0000018 ... P23909 11048711
    435 1e3o:C
    (1.9)
    BS01 >1e3o:A (identical to 7xrc:A, 2xsd:A)
    atgcatgagga
    ? GO:0000981 ... P14859 11583619
    436 1e3o:C
    (1.9)
    BS02 >1e3o:B
    tcctcatgcat
    ? GO:0000981 ... P14859 11583619
    437 1e7j:A
    ()
    BS01 >1e7j:B (identical to 8r1x:B)
    cgatattaagagcc
    ? N/A N/A N/A PDBbind: Kd=1uM
    438 1e7j:A
    ()
    BS02 >1e7j:C (identical to 8r1x:C)
    ggctcaatatcg
    ? N/A N/A N/A PDBbind: Kd=1uM
    439 1ea4:A
    (2.95)
    BS01 >1ea4:Y
    aaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    440 1ea4:A
    (2.95)
    BS02 >1ea4:Z (identical to 1ea4:V)
    agattgcattgagtgcacggt
    ? GO:0003677 ... P13920 11428897
    441 1ea4:B
    (2.95)
    BS01 >1ea4:X
    agattgcattgagtgcacggtt
    ? GO:0003677 ... P13920 11428897
    442 1ea4:B
    (2.95)
    BS02 >1ea4:Y
    aaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    443 1ea4:B
    (2.95)
    BS03 >1ea4:Z (identical to 1ea4:V)
    agattgcattgagtgcacggt
    ? GO:0003677 ... P13920 11428897
    444 1ea4:D
    (2.95)
    BS01 >1ea4:W
    taaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    445 1ea4:D
    (2.95)
    BS02 >1ea4:X
    agattgcattgagtgcacggtt
    ? GO:0003677 ... P13920 11428897
    446 1ea4:E
    (2.95)
    BS01 >1ea4:W
    taaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    447 1ea4:E
    (2.95)
    BS02 >1ea4:X
    agattgcattgagtgcacggtt
    ? GO:0003677 ... P13920 11428897
    448 1ea4:F
    (2.95)
    BS01 >1ea4:W
    taaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    449 1ea4:F
    (2.95)
    BS02 >1ea4:X
    agattgcattgagtgcacggtt
    ? GO:0003677 ... P13920 11428897
    450 1ea4:G
    (2.95)
    BS01 >1ea4:W
    taaccgtgcactcaatgcaatc
    ? GO:0003677 ... P13920 11428897
    451 1ea4:G
    (2.95)
    BS02 >1ea4:X
    agattgcattgagtgcacggtt
    ? GO:0003677 ... P13920 11428897
    452 1ea4:H
    (2.95)
    BS01 >1ea4:U
    aaccgtgcactcaatgcaat
    ? GO:0003677 ... P13920 11428897
    453 1ea4:H
    (2.95)
    BS02 >1ea4:V (identical to 1ea4:Z)
    agattgcattgagtgcacggt
    ? GO:0003677 ... P13920 11428897
    454 1ea4:J
    (2.95)
    BS01 >1ea4:U
    aaccgtgcactcaatgcaat
    ? GO:0003677 ... P13920 11428897
    455 1ea4:J
    (2.95)
    BS02 >1ea4:V (identical to 1ea4:Z)
    agattgcattgagtgcacggt
    ? GO:0003677 ... P13920 11428897
    456 1ea4:K
    (2.95)
    BS01 >1ea4:U
    aaccgtgcactcaatgcaat
    ? GO:0003677 ... P13920 11428897
    457 1ea4:L
    (2.95)
    BS01 >1ea4:U
    aaccgtgcactcaatgcaat
    ? GO:0003677 ... P13920 11428897
    458 1ea4:L
    (2.95)
    BS02 >1ea4:V (identical to 1ea4:Z)
    agattgcattgagtgcacggt
    ? GO:0003677 ... P13920 11428897
    459 1ebm:A
    (2.1)
    BS01 >1ebm:C (identical to 1n3c:C, 2nol:C)
    gcgtccaggtctacc
    3.2.2.-
    4.2.99.18
    GO:0000978 ... O15527 10706276
    460 1ebm:A
    (2.1)
    BS02 >1ebm:D (identical to 4ejy:D, 4ejy:F, 1fn7:C, 1hu0:D, 1lwv:D, 1lww:D, 1lwy:D, 1m3h:B, 1m3q:B, 1n39:B, 1n3a:B, 1n3c:B, 2noh:B, 2nol:B, 6w0m:C)
    ggtagacctggacgc
    3.2.2.-
    4.2.99.18
    GO:0000978 ... O15527 10706276
    461 1ecr:A
    (2.7)
    BS01 >1ecr:B (identical to 2ewj:B, 2i05:B, 2i06:B)
    tagttacaacatact
    ? GO:0003677 ... P16525 8857533
    462 1ecr:A
    (2.7)
    BS02 >1ecr:C (identical to 2i05:C)
    tagtatgttgtaact
    ? GO:0003677 ... P16525 8857533
    463 1efa:A
    (2.6)
    BS01 >1efa:D (identical to 2pe5:D)
    tgtgagcgctcacaatt
    ? GO:0000976 ... P03023 10700279
    464 1efa:A
    (2.6)
    BS02 >1efa:E (identical to 2pe5:E, 2pe5:F)
    aattgtgagcgctcaca
    ? GO:0000976 ... P03023 10700279
    465 1efa:B
    (2.6)
    BS01 >1efa:D (identical to 2pe5:D)
    tgtgagcgctcacaatt
    ? GO:0000976 ... P03023 10700279
    466 1efa:B
    (2.6)
    BS02 >1efa:E (identical to 2pe5:E, 2pe5:F)
    aattgtgagcgctcaca
    ? GO:0000976 ... P03023 10700279
    467 1egw:A
    (1.5)
    BS01 >1egw:E (identical to 1egw:H, 3mu6:E, 3mu6:G)
    aaagctattattagctt
    ? GO:0000977 ... Q02078 10715212
    468 1egw:A
    (1.5)
    BS02 >1egw:F (identical to 1egw:G, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    469 1egw:B
    (1.5)
    BS01 >1egw:E (identical to 1egw:H, 3mu6:E, 3mu6:G)
    aaagctattattagctt
    ? GO:0000977 ... Q02078 10715212
    470 1egw:B
    (1.5)
    BS02 >1egw:F (identical to 1egw:G, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    471 1egw:B
    (1.5)
    BS03 >1egw:G (identical to 1egw:F, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    472 1egw:C
    (1.5)
    BS01 >1egw:F (identical to 1egw:G, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    473 1egw:C
    (1.5)
    BS02 >1egw:G (identical to 1egw:F, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    474 1egw:C
    (1.5)
    BS03 >1egw:H (identical to 1egw:E, 3mu6:E, 3mu6:G)
    aaagctattattagctt
    ? GO:0000977 ... Q02078 10715212
    475 1egw:D
    (1.5)
    BS01 >1egw:G (identical to 1egw:F, 3mu6:F, 3mu6:H)
    taagctaataatagctt
    ? GO:0000977 ... Q02078 10715212
    476 1egw:D
    (1.5)
    BS02 >1egw:H (identical to 1egw:E, 3mu6:E, 3mu6:G)
    aaagctattattagctt
    ? GO:0000977 ... Q02078 10715212
    477 1ehl:H
    (2.4)
    BS01 >1ehl:A (identical to 1i8m:D, 6j7y:C, 5k97:G, 6kcp:E, 3px7:B, 7q8a:E, 1rh0:D, 1rh0:F, 3u7h:X, 6wg6:M, 6wg6:N, 1xhz:F)
    tt
    ? N/A P01863 10835279
    478 1ehl:L
    (2.4)
    BS01 >1ehl:A (identical to 1i8m:D, 6j7y:C, 5k97:G, 6kcp:E, 3px7:B, 7q8a:E, 1rh0:D, 1rh0:F, 3u7h:X, 6wg6:M, 6wg6:N, 1xhz:F)
    tt
    ? GO:0005576 ... P01837 10835279
    479 1ej9:A
    (2.6)
    BS01 >1ej9:C
    aaaaagactcagaaaaattttt
    5.6.2.1 GO:0003677 ... P11387 10841763
    480 1ej9:A
    (2.6)
    BS02 >1ej9:D
    aaaaatttttctgagtcttttt
    5.6.2.1 GO:0003677 ... P11387 10841763
    481 1emh:A
    (1.8)
    BS01 >1emh:B
    tgtuatctt
    3.2.2.27 GO:0004844 ... P13051 10805771
    482 1emj:A
    (2.0)
    BS01 >1emj:B (identical to 2oyt:B, 1q3f:B)
    tgtcatctt
    3.2.2.27 GO:0004844 ... P13051 10805771
    483 1emj:A
    (2.0)
    BS02 >1emj:C
    aaagataaca
    3.2.2.27 GO:0004844 ... P13051 10805771
    484 1eo3:A
    (2.0)
    BS01 >1eo3:C (identical to 1eo4:C, 1suz:C, 1sx8:C)
    aagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    485 1eo3:A
    (2.0)
    BS02 >1eo3:D (identical to 1eon:D)
    caagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    486 1eo3:B
    (2.0)
    BS01 >1eo3:C (identical to 1eo4:C, 1suz:C, 1sx8:C)
    aagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    487 1eo3:B
    (2.0)
    BS02 >1eo3:D (identical to 1eon:D)
    caagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    488 1eo4:A
    (1.9)
    BS01 >1eo4:C (identical to 1eo3:C, 1suz:C, 1sx8:C)
    aagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    489 1eo4:A
    (1.9)
    BS02 >1eo4:D (identical to 1suz:D, 1sx8:D)
    caagatatct
    3.1.21.4 GO:0003677 ... P04390 N/A
    490 1eo4:B
    (1.9)
    BS01 >1eo4:C (identical to 1eo3:C, 1suz:C, 1sx8:C)
    aagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    491 1eo4:B
    (1.9)
    BS02 >1eo4:D (identical to 1suz:D, 1sx8:D)
    caagatatct
    3.1.21.4 GO:0003677 ... P04390 N/A
    492 1eon:A
    (1.6)
    BS01 >1eon:C (identical to 1az0:C, 1az0:D, 1b94:C, 1b94:D, 1b95:C, 1b95:D, 1b96:C, 1b96:D, 1b97:C, 1b97:D, 1bss:C, 1bss:D, 2ge5:C, 2ge5:D, 1rv5:C, 1rv5:D, 1rva:C, 1rva:D, 1rvb:C, 1rvb:D)
    aaagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    493 1eon:A
    (1.6)
    BS02 >1eon:D (identical to 1eo3:D)
    caagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    494 1eon:B
    (1.6)
    BS01 >1eon:C (identical to 1az0:C, 1az0:D, 1b94:C, 1b94:D, 1b95:C, 1b95:D, 1b96:C, 1b96:D, 1b97:C, 1b97:D, 1bss:C, 1bss:D, 2ge5:C, 2ge5:D, 1rv5:C, 1rv5:D, 1rva:C, 1rva:D, 1rvb:C, 1rvb:D)
    aaagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    495 1eon:B
    (1.6)
    BS02 >1eon:D (identical to 1eo3:D)
    caagatatctt
    3.1.21.4 GO:0003677 ... P04390 N/A
    496 1eoo:A
    (2.16)
    BS01 >1eoo:C (identical to 1eoo:D)
    gaagatatcttc
    3.1.21.4 GO:0003677 ... P04390 10801972
    497 1eoo:A
    (2.16)
    BS02 >1eoo:D (identical to 1eoo:C)
    gaagatatcttc
    3.1.21.4 GO:0003677 ... P04390 10801972
    498 1eoo:B
    (2.16)
    BS01 >1eoo:C (identical to 1eoo:D)
    gaagatatcttc
    3.1.21.4 GO:0003677 ... P04390 10801972
    499 1eoo:B
    (2.16)
    BS02 >1eoo:D (identical to 1eoo:C)
    gaagatatcttc
    3.1.21.4 GO:0003677 ... P04390 10801972
    500 1eop:A
    (2.6)
    BS01 >1eop:C (identical to 1eop:D)
    aagatatctta
    3.1.21.4 GO:0003677 ... P04390 10801972

    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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