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 2.07 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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 2.07: 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