PDB entry 5bke

View 5bke on RCSB PDB site
Description: Crystal structure of AAD-2 in complex with Mn(II) and N-oxalylglycine
Class: oxidoreductase
Keywords: dioxygenase, herbicide degradation, OXIDOREDUCTASE
Deposited on 2019-06-02, released 2019-06-12
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-07-17, with a file datestamp of 2019-07-12.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkea_
  • Chain 'B':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkeb_
  • Chain 'C':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkec_
  • Chain 'D':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bked_
  • Chain 'E':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkee_
  • Chain 'F':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkef_
  • Chain 'G':
    Compound: Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase
    Species: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [TaxId:224911]
    Gene: tfdA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5bkeg_
  • Heterogens: MN, OGA, K, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5bkeA (A:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeA (A:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredglndvsnlgkdgkplakdsrthlfnlgnclwhsdssfrpipakfsllsarvvn
    ptggntefadmraaydalddetkaeiedlvcehslmysrgslgfteytdeekqmfkpvlq
    rlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatqpefvyvhkwklhdlvm
    wdnrqtmhrvrrydqsqprdmrratvagteptvqq
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5bkeB (B:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeB (B:)
    iairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafalnf
    gqredrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssfrpipakfsllsarv
    vnptggntefadmraaydalddetkaeiedlvcehslmysrgslgfteytdeekqmfkpv
    lqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatqpefvyvhkwklhdl
    vmwdnrqtmhrvrrydqsqprdmrratvagteptvqq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5bkeC (C:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeC (C:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptv
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5bkeD (D:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeD (D:)
    airqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafalnfg
    qredsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssfrpipakfsllsarvvnpt
    ggntefadmraaydalddetkaeiedlvcehslmysrgslgfteytdeekqmfkpvlqrl
    vrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatqpefvyvhkwklhdlvmwd
    nrqtmhrvrrydqsqprdmrratvagteptv
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5bkeE (E:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeE (E:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqreglndvsnllgnclwhsdssfrpipakfsllsarvvnptggntefadmraaydal
    ddetkaeiedlvcehslmysrgslgfteytdeekqmfkpvlqrlvrthpvhrrkslylss
    hagkiasmsvpegrlllrdlnehatqpefvyvhkwklhdlvmwdnrqtmhrvrrydqsqp
    rdmrratvagteptv
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5bkeF (F:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeF (F:)
    tiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafaln
    fgqrethlfnlgnclwhsdssfrpipakfsllsarvvnptggntefadmraaydalddet
    kaeiedlvcehslmysrgslgfteytdeekqmfkpvlqrlvrthpvhrrkslylsshagk
    iasmsvpegrlllrdlnehatqpefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmr
    ratvagteptvq
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5bkeG (G:)
    mtiairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafal
    nfgqredarggtvtkekdyrlqsglndvsnlgkdgkplakdsrthlfnlgnclwhsdssf
    rpipakfsllsarvvnptggntefadmraaydalddetkaeiedlvcehslmysrgslgf
    teytdeekqmfkpvlqrlvrthpvhrrkslylsshagkiasmsvpegrlllrdlnehatq
    pefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmrratvagteptvqqqaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5bkeG (G:)
    iairqlqthfvgqvsgldlrkpltpgearevesamdkyavlvfhdqditdeqqmafalnf
    gqredthlfnlgnclwhsdssfrpipakfsllsarvvnptggntefadmraaydalddet
    kaeiedlvcehslmysrgslgfteytdeekqmfkpvlqrlvrthpvhrrkslylsshagk
    iasmsvpegrlllrdlnehatqpefvyvhkwklhdlvmwdnrqtmhrvrrydqsqprdmr
    ratvagteptvq