PDB entry 5ysh

View 5ysh on RCSB PDB site
Description: Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal
Class: lyase
Keywords: Adenosylcobalamin, Radical enzyme, LYASE
Deposited on 2017-11-14, released 2018-09-19
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-09-19, with a file datestamp of 2018-09-14.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: N/A
AEROSPACI score: 0.34 (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):
    • Uniprot Q59470 (0-End)
      • engineered mutation (171)
    Domains in SCOPe 2.07: d5ysha_
  • Chain 'B':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5yshb_
  • 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 2.07: d5yshc_
  • 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):
    • Uniprot Q59470 (0-End)
      • engineered mutation (171)
    Domains in SCOPe 2.07: d5yshd_
  • Chain 'E':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5yshe_
  • 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 2.07: d5yshf_
  • 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):
    • Uniprot Q59470 (0-End)
      • engineered mutation (171)
    Domains in SCOPe 2.07: d5yshg_
  • Chain 'H':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q59471 (21-End)
      • expression tag (19-20)
    Domains in SCOPe 2.07: d5yshh1, d5yshh2
  • 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 2.07: d5yshi_
  • 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):
    • Uniprot Q59470 (0-End)
      • engineered mutation (171)
    Domains in SCOPe 2.07: d5yshj_
  • Chain 'K':
    Compound: diol dehydrase beta subunit
    Species: Klebsiella oxytoca [TaxId:571]
    Gene: pddB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5yshk_
  • 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 2.07: d5yshl_
  • Heterogens: CA, K, PGO, 5AD, B12, HOH

PDB Chain Sequences:

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshB (B:)
gfltevgearqgtqqdeviiavgpafglaqtvnivgiphksilreviagieeegikarvi
rcfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltlety
rqigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrv

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshD (D:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqetavavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldp

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshE (E:)
fltevgearqtqqdeviiavgpafglaqtvnivgiphksilreviagieeegikarvirc
fkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltletyrq
igknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrva

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshG (G:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqetavavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldp

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshH (H:)
pggfltevgearqgtqqdeviiavgpafglaqtvnivgiphksilreviagieeegikar
vircfkssdvafvavegnrlsgsgisigiqskgttvihqqglpplsnlelfpqaplltle
tyrqigknaaryakrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrva

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshJ (J:)
mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd
lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm
nvvemmmamqkmrarrtpsqqahvtnvkdnpvqiaadaaegawrgfdeqetavavaryap
fnaiallvgsqvgrpgvltqcsleeatelklgmlghtcyaetisvygtepvftdgddtpw
skgflassyasrglkmrftsgsgsevqmgyaegksmlylearciyitkaagvqglqngsv
scigvpsavpsgiravlaenlicssldlecassndqtfthsdmrrtarllmqflpgtdfi
ssgysavpnydnmfagsnedaedfddynviqrdlkvdgglrpvreedviairnkaaralq
avfagmglppitdeeveaatyahgskdmpernivedikfaqeiinknrnglevvkalaqg
gftdvaqdmlniqkakltgdylhtsaiivgdgqvlsavndvndyagpatgyrlqgerwee
iknipgaldpn

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5yshK (K:)
tevgearqqdeviiavgpafglaqtvnivgiphksilreviagieeegikarvircfkss
dvafvavegnrlsgsgisigiqskgttvihpplsnlelfpqaplltletyrqigknaary
akrespqpvptlndqmarpkyqaksailhiketkyvvtgknpqelrv

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

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