PDB entry 3vdc

View 3vdc on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG
Class: hydrolase
Keywords: transition state stabilization, substrate binding, 2-stage binding, TIM barrel (alpha/beta barrel), jelly-roll barrel, immunoglobulin, beta supersandwich, glycosidase, HYDROLASE
Deposited on 2012-01-04, released 2012-04-11
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-06-19, with a file datestamp of 2013-06-14.
Experiment type: XRAY
Resolution: 2.55 Å
R-factor: 0.179
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (37-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vdca1, d3vdca2, d3vdca3, d3vdca4, d3vdca5
  • Chain 'B':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (37-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vdcb1, d3vdcb2, d3vdcb3, d3vdcb4, d3vdcb5
  • Chain 'C':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (37-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vdcc1, d3vdcc2, d3vdcc3, d3vdcc4, d3vdcc5
  • Chain 'D':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (37-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vdcd1, d3vdcd2, d3vdcd3, d3vdcd4, d3vdcd5
  • Heterogens: IPT, MG, NA, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vdcA (A:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgtesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vdcA (A:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgtesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3vdcB (B:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgtesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vdcB (B:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgtesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3vdcC (C:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgtesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vdcC (C:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgtesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vdcD (D:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgtesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vdcD (D:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgtesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk