PDB entry 2dgk

View 2dgk on RCSB PDB site
Description: Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)
Class: lyase
Keywords: GadB, GadBD1-14, autoinhibition, substituted aldamine, 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 2011-05-08.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: 0.218
AEROSPACI score: 0.45 (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: d2dgka_
  • 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: d2dgkb_
  • 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: d2dgkc_
  • 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: d2dgkd_
  • 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: d2dgke_
  • 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: d2dgkf_
  • Heterogens: SO4, PLP, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dgkA (A:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkA (A:)
    skrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidke
    eypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaa
    gkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvpt
    fgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvk
    sisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqy
    yeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedp
    gytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyl
    sdhpklqgiaqqnsfkht
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dgkB (B:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkB (B:)
    skrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidke
    eypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaa
    gkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvpt
    fgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvk
    sisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqy
    yeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedp
    gytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyl
    sdhpklqgiaqqnsfkht
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2dgkC (C:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkC (C:)
    krfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidkee
    ypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaag
    kptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvptf
    gvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvks
    isasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqyy
    eflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedpg
    ytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyls
    dhpklqgiaqqnsfkht
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2dgkD (D:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkD (D:)
    skrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidke
    eypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaa
    gkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvpt
    fgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvk
    sisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqy
    yeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedp
    gytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyl
    sdhpklqgiaqqnsfkht
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2dgkE (E:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkE (E:)
    skrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidke
    eypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaa
    gkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvpt
    fgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvk
    sisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqy
    yeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedp
    gytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyl
    sdhpklqgiaqqnsfkht
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2dgkF (F:)
    dsrfgaksistiaeskrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhk
    lmdlsinknwidkeeypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlgg
    mamkwrwrkrmeaagkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrm
    ieacdentigvvptfgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfv
    apdivwdfrlprvksisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfa
    infsrpagqviaqyyeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdeg
    ipavcfklkdgedpgytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfa
    ellledykaslkylsdhpklqgiaqqnsfkht
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dgkF (F:)
    skrfplhemrddvafqiindelyldgnarqnlatfcqtwddenvhklmdlsinknwidke
    eypqsaaidlrcvnmvadlwhapapkngqavgtntigsseacmlggmamkwrwrkrmeaa
    gkptdkpnlvcgpvqicwhkfarywdvelreipmrpgqlfmdpkrmieacdentigvvpt
    fgvtytgnyefpqplhdaldkfqadtgididmhidaasggflapfvapdivwdfrlprvk
    sisasghkfglaplgcgwviwrdeealpqelvfnvdylggqigtfainfsrpagqviaqy
    yeflrlgregytkvqnasyqvaayladeiaklgpyefictgrpdegipavcfklkdgedp
    gytlydlserlrlrgwqvpaftlggeatdivvmrimcrrgfemdfaellledykaslkyl
    sdhpklqgiaqqnsfkht