PDB entry 3vd5

View 3vd5 on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460S)
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: 2.7 Å
R-factor: 0.206
AEROSPACI score: 0.28 (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 (Start-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vd5a1, d3vd5a2, d3vd5a3, d3vd5a4, d3vd5a5
  • Chain 'B':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (Start-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vd5b1, d3vd5b2, d3vd5b3, d3vd5b4, d3vd5b5
  • Chain 'C':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (Start-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vd5c1, d3vd5c2, d3vd5c3, d3vd5c4, d3vd5c5
  • Chain 'D':
    Compound: beta-galactosidase
    Species: Escherichia coli [TaxId:562]
    Gene: lacZ
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00722 (Start-1051)
      • engineered mutation (488)
    Domains in SCOPe 2.07: d3vd5d1, d3vd5d2, d3vd5d3, d3vd5d4, d3vd5d5
  • Heterogens: MG, NA, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vd5A (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)
    >3vd5A (A:)
    rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
    wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
    wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
    dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
    ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
    velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
    vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
    lpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyegggad
    ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
    wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
    phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
    apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
    ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
    igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
    rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
    acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
    rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3vd5B (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)
    >3vd5B (B:)
    rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
    wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
    wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
    dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
    ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
    velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
    vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
    lpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyegggad
    ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
    wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
    phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
    apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
    ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
    igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
    rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
    acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
    rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3vd5C (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)
    >3vd5C (C:)
    rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
    wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
    wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
    dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
    ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
    velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
    vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
    lpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyegggad
    ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
    wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
    phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
    apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
    ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
    igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
    rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
    acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
    rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vd5D (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)
    >3vd5D (D:)
    rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
    wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
    wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
    dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
    ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
    velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
    vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
    lpamservtrmvqrdrnhpsviiwslgsesghganhdalyrwiksvdpsrpvqyegggad
    ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
    wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
    phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
    apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
    ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
    igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
    rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
    acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
    rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk