PDB entry 5vta

View 5vta on RCSB PDB site
Description: Co-Crystal Structure of DPPIV with a Chemibody Inhibitor
Class: hydrolase
Keywords: hydrolase, chemibody
Deposited on 2017-05-16, released 2018-05-09
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: dipeptidyl peptidase 4
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Dpp4, Cd26
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5vtaa1, d5vtaa2
  • Chain 'B':
    Compound: dipeptidyl peptidase 4
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Dpp4, Cd26
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5vtab1, d5vtab2
  • Chain 'C':
    Compound: dipeptidyl peptidase 4
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Dpp4, Cd26
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5vtac1, d5vtac2
  • Chain 'D':
    Compound: dipeptidyl peptidase 4
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Dpp4, Cd26
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5vtad1, d5vtad2
  • Chain 'E':
    Compound: Fab light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-End)
    Domains in SCOPe 2.08: d5vtae1, d5vtae2
  • Chain 'F':
    Compound: Fab heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-216)
    Domains in SCOPe 2.08: d5vtaf_
  • Chain 'G':
    Compound: Fab light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-End)
    Domains in SCOPe 2.08: d5vtag_
  • Chain 'H':
    Compound: Fab heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-216)
    Domains in SCOPe 2.08: d5vtah_
  • Chain 'I':
    Compound: Fab heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA
    Domains in SCOPe 2.08: d5vtai_
  • Chain 'J':
    Compound: Fab light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-End)
    Domains in SCOPe 2.08: d5vtaj_
  • Chain 'K':
    Compound: Fab heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA
    Domains in SCOPe 2.08: d5vtak_
  • Chain 'L':
    Compound: Fab light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VTA (0-End)
    Domains in SCOPe 2.08: d5vtal1, d5vtal2
  • Heterogens: NAG, PG4, PEG, EDO, 9K4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5vtaA (A:)
    srrtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeif
    gdsisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitws
    qeghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwsp
    ngtflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslss
    ttttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwn
    cpttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvct
    fitkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercq
    yysvslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkld
    fivlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniiv
    asfdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyv
    tsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenf
    kqveyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshm
    shflqqcfslrhhhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaA (A:)
    rtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeifgd
    sisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitwsqe
    ghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwspng
    tflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslsstt
    ttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwncp
    ttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvctfi
    tkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercqyy
    svslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkldfi
    vlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniivas
    fdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyvts
    mvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkq
    veyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshmsh
    flqqcfsl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5vtaB (B:)
    srrtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeif
    gdsisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitws
    qeghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwsp
    ngtflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslss
    ttttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwn
    cpttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvct
    fitkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercq
    yysvslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkld
    fivlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniiv
    asfdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyv
    tsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenf
    kqveyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshm
    shflqqcfslrhhhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaB (B:)
    rtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeifgd
    sisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitwsqe
    ghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwspng
    tflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslsstt
    ttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdyvwncpttqeh
    ietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdvctfitkgawevisi
    ealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercqyysvslskeaky
    yqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkldfivlnetrfwyq
    milpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniivasfdgrgsgyqg
    dkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyvtsmvlgsgsgvf
    kcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkqveyllihgta
    ddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshmshflqqcfsl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5vtaC (C:)
    srrtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeif
    gdsisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitws
    qeghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwsp
    ngtflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslss
    ttttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwn
    cpttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvct
    fitkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercq
    yysvslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkld
    fivlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniiv
    asfdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyv
    tsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenf
    kqveyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshm
    shflqqcfslrhhhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaC (C:)
    rtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeifgd
    sisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitwsqe
    ghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwspng
    tflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslsstt
    ttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwncp
    ttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvctfi
    tkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercqyy
    svslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkldfi
    vlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniivas
    fdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyvts
    mvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkq
    veyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshmsh
    flqqcfsl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5vtaD (D:)
    srrtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeif
    gdsisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitws
    qeghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwsp
    ngtflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslss
    ttttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwn
    cpttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvct
    fitkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercq
    yysvslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkld
    fivlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniiv
    asfdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyv
    tsmvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenf
    kqveyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshm
    shflqqcfslrhhhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaD (D:)
    rtytladylkntfrvksyslrwvsdseylykqennillfnaehgnssiflenstfeifgd
    sisdysvspdrlfvlleynyvkqwrhsytasysiydlnkrqliteekipnntqwitwsqe
    ghklayvwkndiyvkiephlpshritstgkenvifngindwvyeeeifgaysalwwspng
    tflayaqfndtgvplieysfysdeslqypktvwipypkagavnptvkffivntdslsstt
    ttipmqitapasvttgdhylcdvawvsedrislqwlrriqnysvmaicdydkttlvwncp
    ttqehietsatgwcgrfrpaephftsdgssfykivsdkdgykhicqfqkdrkpeqvctfi
    tkgawevisiealtsdylyyisneykempggrnlykiqltdhtnkkclscdlnpercqyy
    svslskeakyyqlgcrgpglplytlhrstdqkelrvlednsaldkmlqdvqmpskkldfi
    vlnetrfwyqmilpphfdkskkypllidvyagpcsqkadaafrlnwatylasteniivas
    fdgrgsgyqgdkimhainkrlgtlevedqieaarqflkmgfvdskrvaiwgwsyggyvts
    mvlgsgsgvfkcgiavapvsrweyydsvyterymglptpednldhyrnstvmsraenfkq
    veyllihgtaddnvhfqqsaqiskalvdagvdfqamwytdedhgiasstahqhiyshmsh
    flqqcfs
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5vtaE (E:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaE (E:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvlqsgnsqesvteqdskdstyslsstltlska
    dyekhkvyacevthqglsspvtks
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5vtaF (F:)
    efqlqqsgpelvkpgasvkisckasgysftdyninwmkqsngkslewigvvipkygttny
    nqkfqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvtvssastk
    gpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5vtaG (G:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaG (G:)
    qivlsqspailsaspkvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvrfs
    gsgsgtsfsltrveaedaatyfcqqwsnhpptfgggtkle
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5vtaH (H:)
    efqlqqsgpelvkpgasvkisckasgysftdyninwmkqsngkslewigvvipkygttny
    nqkfqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvtvssastk
    gpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >5vtaI (I:)
    efqlqqsgpelvkpgasvkisckasgysftdyninwmkqsngkslewigvvipkygttny
    nqkfqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvtvssastk
    gpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaI (I:)
    fqlqqsgpelvkpgasvkisckasgysftdyninwmkqsngkslewigvvipkygttnyn
    qkfqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvtvss
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5vtaJ (J:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaJ (J:)
    qivlsqspaikvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvrfsgsgsg
    tsfsltisrveatyfcqqwsnhpptfggg
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >5vtaK (K:)
    efqlqqsgpelvkpgasvkisckasgysftdyninwmkqsngkslewigvvipkygttny
    nqkfqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvtvssastk
    gpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaK (K:)
    fqlqqsgpelvkpgasvkisckasgysftninwmkqsngkslewigvvipkygttnynqk
    fqgkatltvdqssstayiqlnsltsedsavyyctrfrvffdvwgtgttvt
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >5vtaL (L:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vtaL (L:)
    qivlsqspailsaspgekvtmtcrasssvcnmhwyqqkpgsspkpwlhgtsnlasgvpvr
    fsgsgsgtsfsltisrveaedaatyfcqqwsnhpptfgggtkleidrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhkvyacevthqglsspvtksf