PDB entry 2dgm

View 2dgm on RCSB PDB site
Description: Crystal structure of Escherichia coli GadB in complex with iodide
Class: lyase
Keywords: GadB complexed with iodide, LYASE
Deposited on 2006-03-14, released 2006-06-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: 0.227
AEROSPACI score: 0.43 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgma_
  • Chain 'B':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgmb_
  • Chain 'C':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgmc_
  • Chain 'D':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgmd_
  • Chain 'E':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgme_
  • Chain 'F':
    Compound: Glutamate decarboxylase beta
    Species: Escherichia coli [TaxId:562]
    Gene: gadB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2dgmf_
  • Heterogens: IOD, PLP, FMT, ACY, PEG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dgmA (A:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmA (A:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhpkl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dgmB (B:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmB (B:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhpk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2dgmC (C:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmC (C:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhpklqg
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2dgmD (D:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmD (D:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhpklqg
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2dgmE (E:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmE (E:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhp
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2dgmF (F:)
    mdkkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnl
    atfcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavg
    tntigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelrei
    pmrpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididm
    hidaasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelv
    fnvdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiakl
    gpyefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivv
    mrimcrrgfemdfaellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgmF (F:)
    kkqvtdlrselldsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlat
    fcqtwddenvhklmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtn
    tigsseacmlggmamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipm
    rpgqlfmdpkrmieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhi
    daasggflapfvapdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfn
    vdylggqigtfainfsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgp
    yefictgrpdegipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmr
    imcrrgfemdfaellledykaslkylsdhpklqg