PDB entry 3ccb

View 3ccb on RCSB PDB site
Description: Crystal Structure of Human DPP4 in complex with a benzimidazole derivative
Class: hydrolase
Keywords: structure-based design, denzimidazole derivatives, peptidase, Aminopeptidase, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine protease, Signal-anchor, Transmembrane
Deposited on 2008-02-25, released 2008-10-21
The last revision prior to the SCOP 1.75 freeze date was dated 2008-10-21, with a file datestamp of 2008-10-17.
Experiment type: XRAY
Resolution: 2.49 Å
R-factor: 0.202
AEROSPACI score: 0.38 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: dipeptidyl peptidase 4
    Species: HOMO SAPIENS
    Gene: DPP4, ADCP2, CD26
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3ccba1, d3ccba2
  • Chain 'B':
    Compound: dipeptidyl peptidase 4
    Species: HOMO SAPIENS
    Gene: DPP4, ADCP2, CD26
    Database cross-references and differences (RAF-indexed):
    • Uniprot P27487 (12-739)
      • expression tag (9-11)
    Domains in SCOP 1.75: d3ccbb1, d3ccbb2
  • Chain 'C':
    Compound: dipeptidyl peptidase 4
    Species: HOMO SAPIENS
    Gene: DPP4, ADCP2, CD26
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3ccbc1, d3ccbc2
  • Chain 'D':
    Compound: dipeptidyl peptidase 4
    Species: HOMO SAPIENS
    Gene: DPP4, ADCP2, CD26
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3ccbd1, d3ccbd2
  • Heterogens: NAG, B2Y, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3ccbA (A:)
    adpggshhhhhhsrktytltdylkntyrlklyslrwisdheylykqennilvfnaeygns
    svflenstfdefghsindysispdgqfilleynyvkqwrhsytasydiydlnkrqlitee
    ripnntqwvtwspvghklayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeee
    vfsaysalwwspngtflayaqfndtevplieysfysdeslqypktvrvpypkagavnptv
    kffvvntdslssvtnatsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmd
    icdydessgrwnclvarqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicy
    fqidkkdctfitkgtwevigiealtsdylyyisneykgmpggrnlykiqlsdytkvtcls
    celnpercqyysvsfskeakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqn
    vqmpskkldfiilnetkfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwaty
    lasteniivasfdgrgsgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriai
    wgwsyggyvtsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrns
    tvmsraenfkqveyllihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasst
    ahqhiythmshfikqcfslp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ccbA (A:)
    ktytltdylkntyrlklyslrwisdheylykqnilvfnaeygnssvflenstfdefghsi
    ndysispdgqfilleynyvkqwrhsytasydiydlnkrqliteeripnntqwvtwspvgh
    klayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeeevfsaysalwwspngtf
    layaqfndtevplieysfysdeslqypktvrvpypkagavnptvkffvvntdslssvtna
    tsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmdicdydessgrwnclva
    rqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicyfqidkkdctfitkgtw
    evigiealtsdylyyisneykgmpggrnlykiqlsdytkvtclscelnpercqyysvsfs
    keakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqnvqmpskkldfiilnet
    kfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwatylasteniivasfdgrg
    sgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriaiwgwsyggyvtsmvlgs
    gsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkqveyll
    ihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasstahqhiythmshfikqc
    fslp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3ccbB (B:)
    adpggshhhhhhsrktytltdylkntyrlklyslrwisdheylykqennilvfnaeygns
    svflenstfdefghsindysispdgqfilleynyvkqwrhsytasydiydlnkrqlitee
    ripnntqwvtwspvghklayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeee
    vfsaysalwwspngtflayaqfndtevplieysfysdeslqypktvrvpypkagavnptv
    kffvvntdslssvtnatsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmd
    icdydessgrwnclvarqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicy
    fqidkkdctfitkgtwevigiealtsdylyyisneykgmpggrnlykiqlsdytkvtcls
    celnpercqyysvsfskeakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqn
    vqmpskkldfiilnetkfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwaty
    lasteniivasfdgrgsgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriai
    wgwsyggyvtsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrns
    tvmsraenfkqveyllihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasst
    ahqhiythmshfikqcfslp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ccbB (B:)
    hhhsrktytltdylkntyrlklyslrwisdheylykqnilvfnaeygnssvflenstfde
    fghsindysispdgqfilleynyvkqwrhsytasydiydlnkrqliteeripnntqwvtw
    spvghklayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeeevfsaysalwws
    pngtflayaqfndtevplieysfysdeslqypktvrvpypkagavnptvkffvvntdsls
    svtnatsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmdicdydessgrw
    nclvarqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicyfqidkkdctfi
    tkgtwevigiealtsdylyyisneykgmpggrnlykiqlsdytkvtclscelnpercqyy
    svsfskeakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqnvqmpskkldfi
    ilnetkfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwatylasteniivas
    fdgrgsgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriaiwgwsyggyvts
    mvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkq
    veyllihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasstahqhiythmsh
    fikqcfslp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3ccbC (C:)
    adpggshhhhhhsrktytltdylkntyrlklyslrwisdheylykqennilvfnaeygns
    svflenstfdefghsindysispdgqfilleynyvkqwrhsytasydiydlnkrqlitee
    ripnntqwvtwspvghklayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeee
    vfsaysalwwspngtflayaqfndtevplieysfysdeslqypktvrvpypkagavnptv
    kffvvntdslssvtnatsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmd
    icdydessgrwnclvarqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicy
    fqidkkdctfitkgtwevigiealtsdylyyisneykgmpggrnlykiqlsdytkvtcls
    celnpercqyysvsfskeakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqn
    vqmpskkldfiilnetkfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwaty
    lasteniivasfdgrgsgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriai
    wgwsyggyvtsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrns
    tvmsraenfkqveyllihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasst
    ahqhiythmshfikqcfslp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ccbC (C:)
    ktytltdylkntyrlklyslrwisdheylykqnilvfnaeygnssvflenstfdefghsi
    ndysispdgqfilleynyvkqwrhsytasydiydlnkrqliteeripnntqwvtwspvgh
    klayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeeevfsaysalwwspngtf
    layaqfndtevplieysfysdeslqypktvrvpypkagavnptvkffvvntdslssvtna
    tsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmdicdydessgrwnclva
    rqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicyfqidkkdctfitkgtw
    evigiealtsdylyyisneykgmpggrnlykiqlsdytkvtclscelnpercqyysvsfs
    keakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqnvqmpskkldfiilnet
    kfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwatylasteniivasfdgrg
    sgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriaiwgwsyggyvtsmvlgs
    gsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkqveyll
    ihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasstahqhiythmshfikqc
    fslp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3ccbD (D:)
    adpggshhhhhhsrktytltdylkntyrlklyslrwisdheylykqennilvfnaeygns
    svflenstfdefghsindysispdgqfilleynyvkqwrhsytasydiydlnkrqlitee
    ripnntqwvtwspvghklayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeee
    vfsaysalwwspngtflayaqfndtevplieysfysdeslqypktvrvpypkagavnptv
    kffvvntdslssvtnatsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmd
    icdydessgrwnclvarqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicy
    fqidkkdctfitkgtwevigiealtsdylyyisneykgmpggrnlykiqlsdytkvtcls
    celnpercqyysvsfskeakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqn
    vqmpskkldfiilnetkfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwaty
    lasteniivasfdgrgsgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriai
    wgwsyggyvtsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrns
    tvmsraenfkqveyllihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasst
    ahqhiythmshfikqcfslp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ccbD (D:)
    ktytltdylkntyrlklyslrwisdheylykqnilvfnaeygnssvflenstfdefghsi
    ndysispdgqfilleynyvkqwrhsytasydiydlnkrqliteeripnntqwvtwspvgh
    klayvwnndiyvkiepnlpsyritwtgkediiyngitdwvyeeevfsaysalwwspngtf
    layaqfndtevplieysfysdeslqypktvrvpypkagavnptvkffvvntdslssvtna
    tsiqitapasmligdhylcdvtwatqerislqwlrriqnysvmdicdydessgrwnclva
    rqhiemsttgwvgrfrpsephftldgnsfykiisneegyrhicyfqidkkdctfitkgtw
    evigiealtsdylyyisneykgmpggrnlykiqlsdytkvtclscelnpercqyysvsfs
    keakyyqlrcsgpglplytlhssvndkglrvlednsaldkmlqnvqmpskkldfiilnet
    kfwyqmilpphfdkskkypllldvyagpcsqkadtvfrlnwatylasteniivasfdgrg
    sgyqgdkimhainrrlgtfevedqieaarqfskmgfvdnkriaiwgwsyggyvtsmvlgs
    gsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkqveyll
    ihgtaddnvhfqqsaqiskalvdvgvdfqamwytdedhgiasstahqhiythmshfikqc
    fslp