PDB entry 3vda

View 3vda on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460T)
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 2.04 freeze date was dated 2013-06-19, with a file datestamp of 2013-06-14.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.175
AEROSPACI score: 0.36 (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 2.04: d3vdaa1, d3vdaa2, d3vdaa3, d3vdaa4, d3vdaa5
  • 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 2.04: d3vdab1, d3vdab2, d3vdab3, d3vdab4, d3vdab5
  • 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 2.04: d3vdac1, d3vdac2, d3vdac3, d3vdac4, d3vdac5
  • 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 2.04: d3vdad1, d3vdad2, d3vdad3, d3vdad4, d3vdad5
  • Heterogens: MG, NA, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3vdaA (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) 
    >3vdaA (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) 
    >3vdaB (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) 
    >3vdaB (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) 
    >3vdaC (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) 
    >3vdaC (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) 
    >3vdaD (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) 
    >3vdaD (D:)
vvlqrrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapea
vpeswlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfn
vdeswlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmv
lrwsdgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcg
elrdylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnl
yravvelhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmd
eqtmvqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltd
dprwlpamservtrmvqrdrnhpsviiwslgtesghganhdalyrwiksvdpsrpvqyeg
ggadttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslgg
fakywqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvf
adrtphpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgev
pldvapqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsv
tlpaashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrap
ldndigvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgkt
lfisrktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypd
rltaacfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlm
etshrhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk