PDB entry 3vd9

View 3vd9 on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460S) 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 2.06 freeze date was dated 2013-06-19, with a file datestamp of 2013-06-14.
Experiment type: XRAY
Resolution: 2.05 Å
R-factor: 0.17
AEROSPACI score: 0.46 (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 2.06: d3vd9a1, d3vd9a2, d3vd9a3, d3vd9a4, d3vd9a5
  • Chain 'B':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (37-1051)
      • expression tag (36)
      • engineered mutation (488)
    Domains in SCOPe 2.06: d3vd9b1, d3vd9b2, d3vd9b3, d3vd9b4, d3vd9b5, d3vd9b6
  • 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 2.06: d3vd9c1, d3vd9c2, d3vd9c3, d3vd9c4, d3vd9c5
  • 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 2.06: d3vd9d1, d3vd9d2, d3vd9d3, d3vd9d4, d3vd9d5
  • Heterogens: MG, NA, IPT, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vd9A (A:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgsesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vd9A (A:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3vd9B (B:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgsesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vd9B (B:)
    pvvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpape
    avpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltf
    nvdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavm
    vlrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmc
    gelrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipn
    lyravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvm
    deqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrlt
    ddprwlpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqye
    gggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslg
    gfakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglv
    fadrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasge
    vpldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenls
    vtlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftra
    pldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgk
    tlfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenyp
    drltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqql
    metshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3vd9C (C:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgsesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vd9C (C:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vd9D (D:)
    mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
    pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
    mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
    lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
    vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
    apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
    frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
    ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
    sviiwslgsesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
    fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
    dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
    sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
    gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
    gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
    aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
    vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
    psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
    giggddswspsvsaefqlsagryhyqlvwcqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vd9D (D:)
    vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
    vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
    vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
    lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
    elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
    yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
    eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
    dprwlpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyeg
    ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
    fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
    adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
    pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
    tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
    ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
    lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
    rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
    etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk