PDB entry 5ymr

View 5ymr on RCSB PDB site
Description: The Crystal Structure of IseG
Class: lyase
Keywords: Isethionate, glycyl radical enzyme, C-S bond cleavage, LYASE
Deposited on 2017-10-22, released 2019-03-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-03-20, with a file datestamp of 2019-03-15.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Formate acetyltransferase
    Species: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) [TaxId:882]
    Gene: DVU_2824
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q727N1 (Start-807)
      • engineered mutation (112-113)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5ymra_
  • Chain 'B':
    Compound: Formate acetyltransferase
    Species: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) [TaxId:882]
    Gene: DVU_2824
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q727N1 (Start-807)
      • engineered mutation (112-113)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5ymrb_
  • Chain 'C':
    Compound: Formate acetyltransferase
    Species: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) [TaxId:882]
    Gene: DVU_2824
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q727N1 (Start-807)
      • engineered mutation (112-113)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5ymrc_
  • Chain 'D':
    Compound: Formate acetyltransferase
    Species: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) [TaxId:882]
    Gene: DVU_2824
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q727N1 (Start-807)
      • engineered mutation (112-113)
      • engineered mutation (115)
    Domains in SCOPe 2.07: d5ymrd_
  • Heterogens: 8X3, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5ymrA (A:)
    snaryrathervftilesfdntrpridverakyftesmkategqplplrwakalmhiaen
    mtvyiddhqlicgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvve
    eiapfwkgktyhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvl
    krgfrsikeealekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaak
    etdptrkreletmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqy
    fwpfyekdlaegritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggq
    tpegrdatndltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklin
    deevvplyvskgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkml
    kygdtdlgahtgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgss
    lhdlcmkhcldlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgelieal
    kcnfegkediqqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpf
    tshvpfgrvvsatpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarm
    lnikftpkcvegeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivr
    iagysayfvdlspdlqndliartghdvm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ymrA (A:)
    rvftilesfdntrpridverakyftesmkategqplplrwakalmhiaenmtvyiddhql
    icgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvveeiapfwkgkt
    yhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvlkrgfrsikee
    alekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaaketdptrkrel
    etmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqyfwpfyekdla
    egritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggqtpegrdatnd
    ltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklindeevvplyvs
    kgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkmlkygdtdlgah
    tgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgsslhdlcmkhcl
    dlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgeliealkcnfegkedi
    qqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpftshvpfgrvv
    satpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarmlnikftpkcv
    egeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivriagysayfvd
    lspdlqndliartghdvm
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5ymrB (B:)
    snaryrathervftilesfdntrpridverakyftesmkategqplplrwakalmhiaen
    mtvyiddhqlicgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvve
    eiapfwkgktyhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvl
    krgfrsikeealekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaak
    etdptrkreletmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqy
    fwpfyekdlaegritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggq
    tpegrdatndltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklin
    deevvplyvskgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkml
    kygdtdlgahtgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgss
    lhdlcmkhcldlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgelieal
    kcnfegkediqqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpf
    tshvpfgrvvsatpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarm
    lnikftpkcvegeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivr
    iagysayfvdlspdlqndliartghdvm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ymrB (B:)
    rvftilesfdntrpridverakyftesmkategqplplrwakalmhiaenmtvyiddhql
    icgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvveeiapfwkgkt
    yhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvlkrgfrsikee
    alekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaaketdptrkrel
    etmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqyfwpfyekdla
    egritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggqtpegrdatnd
    ltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklindeevvplyvs
    kgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkmlkygdtdlgah
    tgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgsslhdlcmkhcl
    dlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgeliealkcnfegkedi
    qqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpftshvpfgrvv
    satpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarmlnikftpkcv
    egeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivriagysayfvd
    lspdlqndliartghdvm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5ymrC (C:)
    snaryrathervftilesfdntrpridverakyftesmkategqplplrwakalmhiaen
    mtvyiddhqlicgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvve
    eiapfwkgktyhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvl
    krgfrsikeealekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaak
    etdptrkreletmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqy
    fwpfyekdlaegritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggq
    tpegrdatndltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklin
    deevvplyvskgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkml
    kygdtdlgahtgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgss
    lhdlcmkhcldlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgelieal
    kcnfegkediqqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpf
    tshvpfgrvvsatpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarm
    lnikftpkcvegeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivr
    iagysayfvdlspdlqndliartghdvm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ymrC (C:)
    vftilesfdntrpridverakyftesmkategqplplrwakalmhiaenmtvyiddhqli
    cgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvveeiapfwkgkty
    healnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvlkrgfrsikeea
    lekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaaketdptrkrele
    tmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqyfwpfyekdlae
    gritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggqtpegrdatndl
    tylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklindeevvplyvsk
    gatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkmlkygdtdlgaht
    gdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgsslhdlcmkhcld
    lhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgeliealkcnfegkediq
    qllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpftshvpfgrvvs
    atpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarmlnikftpkcve
    geegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivriagysayfvdl
    spdlqndliartghdvm
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5ymrD (D:)
    snaryrathervftilesfdntrpridverakyftesmkategqplplrwakalmhiaen
    mtvyiddhqlicgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvve
    eiapfwkgktyhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvl
    krgfrsikeealekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaak
    etdptrkreletmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqy
    fwpfyekdlaegritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggq
    tpegrdatndltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklin
    deevvplyvskgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkml
    kygdtdlgahtgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgss
    lhdlcmkhcldlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgelieal
    kcnfegkediqqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpf
    tshvpfgrvvsatpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarm
    lnikftpkcvegeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivr
    iagysayfvdlspdlqndliartghdvm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ymrD (D:)
    rvftilesfdntrpridverakyftesmkategqplplrwakalmhiaenmtvyiddhql
    icgragyqgrygvlypeldgdflgtaiedlpnraespfaitpaaaavvveeiapfwkgkt
    yhealnlalpadvhkltyddpqglmsrfivnetssfrssiqwvhdyekvlkrgfrsikee
    alekiaaldpmspcdnvekrpfleaivivcdaiilwakrhaklaaelaaketdptrkrel
    etmaeicawvpenpartfheavqaqwftqvfsrieqktgtivsngrmdqyfwpfyekdla
    egritedsalellecmwvgmaqyvdlyisptggafnegyahweavtiggqtpegrdatnd
    ltylflkskrefplhypdlaarihsrsperylwevaetikdgsgfpklindeevvplyvs
    kgatfaealdyavsgctearmpnrdtytsggayinfaaalemvlyngkmlkygdtdlgah
    tgdpcefktweefwnayvtqhhlflktafvqqhiinnlrarhfaqpmgsslhdlcmkhcl
    dlhtpqipeginlgyfeymgfgtvvdslsaikklvfedkkltmgeliealkcnfegkedi
    qqllksapcygnnddyadsiardidalsvkygrryspelgmhndvryvpftshvpfgrvv
    satpngrkawsalsdgssashgadvngptailqsnfnsknygmrdraarmlnikftpkcv
    egeegsqklvsfirtfcdlklwhvqfnvinketllaaqrdpekyrnlivriagysayfvd
    lspdlqndliartghdvm