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 2.08 freeze date was dated 2019-10-02, with a file datestamp of 2019-09-27.
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 2.08: 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 2.08: 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 2.08: 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 2.08: 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