PDB entry 3vd4

View 3vd4 on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460D) 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 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.39 (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 2.08: d3vd4a1, d3vd4a2, d3vd4a3, d3vd4a4, d3vd4a5
  • 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 2.08: d3vd4b1, d3vd4b2, d3vd4b3, d3vd4b4, d3vd4b5
  • 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 2.08: d3vd4c1, d3vd4c2, d3vd4c3, d3vd4c4, d3vd4c5
  • 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 2.08: d3vd4d1, d3vd4d2, d3vd4d3, d3vd4d4, d3vd4d5
  • Heterogens: MG, NA, DMS, IPT, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3vd4A (A:)
mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
sviiwslgdesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
giggddswspsvsaefqlsagryhyqlvwcqk

    Sequence, based on observed residues (ATOM records): (download) 
    >3vd4A (A:)
vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
dprwlpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyeg
ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3vd4B (B:)
mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
sviiwslgdesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
giggddswspsvsaefqlsagryhyqlvwcqk

    Sequence, based on observed residues (ATOM records): (download) 
    >3vd4B (B:)
vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
dprwlpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyeg
ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3vd4C (C:)
mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
sviiwslgdesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
giggddswspsvsaefqlsagryhyqlvwcqk

    Sequence, based on observed residues (ATOM records): (download) 
    >3vd4C (C:)
vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
dprwlpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyeg
ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3vd4D (D:)
mggshhhhhhgmasmtggqqmgrdlyddddkdpmidpvvlqrrdwenpgvtqlnrlaahp
pfaswrnseeartdrpsqqlrslngewrfawfpapeavpeswlecdlpeadtvvvpsnwq
mhgydapiytnvtypitvnppfvptenptgcysltfnvdeswlqegqtriifdgvnsafh
lwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrwsdgsyledqdmwrmsgifrd
vsllhkpttqisdfhvatrfnddfsravleaevqmcgelrdylrvtvslwqgetqvasgt
apfggeiiderggyadrvtlrlnvenpklwsaeipnlyravvelhtadgtlieaeacdvg
frevriengllllngkpllirgvnrhehhplhgqvmdeqtmvqdillmkqnnfnavrcsh
ypnhplwytlcdryglyvvdeaniethgmvpmnrltddprwlpamservtrmvqrdrnhp
sviiwslgdesghganhdalyrwiksvdpsrpvqyegggadttatdiicpmyarvdedqp
fpavpkwsikkwlslpgetrplilceyahamgnslggfakywqafrqyprlqggfvwdwv
dqslikydengnpwsayggdfgdtpndrqfcmnglvfadrtphpalteakhqqqffqfrl
sgqtievtseylfrhsdnellhwmvaldgkplasgevpldvapqgkqlielpelpqpesa
gqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpaashaiphlttsemdfciel
gnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldndigvseatridpnawverwk
aaghyqaeaallqctadtladavlittahawqhqgktlfisrktyridgsgqmaitvdve
vasdtphpariglncqlaqvaervnwlglgpqenypdrltaacfdrwdlplsdmytpyvf
psenglrcgtrelnygphqwrgdfqfnisrysqqqlmetshrhllhaeegtwlnidgfhm
giggddswspsvsaefqlsagryhyqlvwcqk

    Sequence, based on observed residues (ATOM records): (download) 
    >3vd4D (D:)
vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
dprwlpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyeg
ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk