PDB entry 5yrt

View 5yrt on RCSB PDB site
Description: Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal
Class: lyase
Keywords: Adenosylcobalamin, Radical enzyme, LYASE
Deposited on 2017-11-10, released 2018-09-19
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-09-19, with a file datestamp of 2018-09-14.
Experiment type: XRAY
Resolution: 1.7 Å
R-factor: N/A
AEROSPACI score: 0.4 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: diol dehydrase alpha subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrta_
  • Chain 'B':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q59471 (21-199)
      • expression tag (18-20)
    Domains in SCOPe 2.08: d5yrtb1, d5yrtb2
  • Chain 'C':
    Compound: diol dehydrase gamma subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtc_
  • Chain 'D':
    Compound: diol dehydrase alpha subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtd_
  • Chain 'E':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrte_
  • Chain 'F':
    Compound: diol dehydrase gamma subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtf_
  • Chain 'G':
    Compound: diol dehydrase alpha subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtg_
  • Chain 'H':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrth_
  • Chain 'I':
    Compound: diol dehydrase gamma subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrti_
  • Chain 'J':
    Compound: diol dehydrase alpha subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtj_
  • Chain 'K':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q59471 (21-199)
      • expression tag (18-20)
    Domains in SCOPe 2.08: d5yrtk1, d5yrtk2
  • Chain 'L':
    Compound: diol dehydrase gamma subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yrtl_
  • Heterogens: CA, K, 5AD, CL, B12, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5yrtA (A:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpneid

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtA (A:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpn

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5yrtB (B:)
msshhhhhhsaalevlfqgpggfltevgearqgtqqdeviiavgpafglaqtvnivgiph
ksilreviagieeegikarvircfkssdvafvavegnrlsgsgisigiqskgttvihqqg
lpplsnlelfpqaplltletyrqigknaaryakrespqpvptlndqmarpkyqaksailh
iketkyvvtgknpqelrval

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtB (B:)
gpggfltevgearqgtqqdeviiavgpafglaqtvnivgiphksilreviagieeegika
rvircfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltl
etyrqigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrv
al

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5yrtC (C:)
marvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakda
grdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafv
reaatlyverkklkgdd

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtC (C:)
arvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakdag
rdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafvr
eaatlyverkklkgdd

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5yrtD (D:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpneid

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtD (D:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpn

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5yrtE (E:)
msshhhhhhsaalevlfqgpggfltevgearqgtqqdeviiavgpafglaqtvnivgiph
ksilreviagieeegikarvircfkssdvafvavegnrlsgsgisigiqskgttvihqqg
lpplsnlelfpqaplltletyrqigknaaryakrespqpvptlndqmarpkyqaksailh
iketkyvvtgknpqelrval

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtE (E:)
gfltevgearqgqqdeviiavgpafglaqtvnivgiphksilreviagieeegikarvir
cfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltletyr
qigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrval

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5yrtF (F:)
marvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakda
grdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafv
reaatlyverkklkgdd

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtF (F:)
arvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakdag
rdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafvr
eaatlyverkklkgdd

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yrtG (G:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpneid

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5yrtH (H:)
msshhhhhhsaalevlfqgpggfltevgearqgtqqdeviiavgpafglaqtvnivgiph
ksilreviagieeegikarvircfkssdvafvavegnrlsgsgisigiqskgttvihqqg
lpplsnlelfpqaplltletyrqigknaaryakrespqpvptlndqmarpkyqaksailh
iketkyvvtgknpqelrval

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtH (H:)
gfltevgearqgtqqdeviiavgpafglaqtvnivgiphksilreviagieeegikarvi
rcfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltlety
rqigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrva

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >5yrtI (I:)
marvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakda
grdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafv
reaatlyverkklkgdd

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtI (I:)
arvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakdag
rdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafvr
eaatlyverkklkgdd

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yrtJ (J:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqettvavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpneid

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >5yrtK (K:)
msshhhhhhsaalevlfqgpggfltevgearqgtqqdeviiavgpafglaqtvnivgiph
ksilreviagieeegikarvircfkssdvafvavegnrlsgsgisigiqskgttvihqqg
lpplsnlelfpqaplltletyrqigknaaryakrespqpvptlndqmarpkyqaksailh
iketkyvvtgknpqelrval

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtK (K:)
gpggfltevgearqgtqqdeviiavgpafglaqtvnivgiphksilreviagieeegika
rvircfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltl
etyrqigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrv
al

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >5yrtL (L:)
marvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakda
grdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafv
reaatlyverkklkgdd

    Sequence, based on observed residues (ATOM records): (download) 
    >5yrtL (L:)
arvsdyplankhpewvktatnktlddftlenvlsnkvtaqdmritpetlrlqasiakdag
rdrlamnferaaeltavpddrileiynalrpyrstkeellaiaddlesryqakicaafvr
eaatlyverkklkgdd