PDB entry 3vd3

View 3vd3 on RCSB PDB site
Description: E. coli (lacZ) beta-galactosidase (N460D)
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 2019-07-17, with a file datestamp of 2019-07-12.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.15 (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 2.08: d3vd3a1, d3vd3a2, d3vd3a3, d3vd3a4, d3vd3a5
  • 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 2.08: d3vd3b1, d3vd3b2, d3vd3b3, d3vd3b4, d3vd3b5
  • 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 2.08: d3vd3c1, d3vd3c2, d3vd3c3, d3vd3c4, d3vd3c5
  • 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 2.08: d3vd3d1, d3vd3d2, d3vd3d3, d3vd3d4, d3vd3d5
  • Heterogens: MG, NA, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3vd3A (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) 
    >3vd3A (A:)
rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
lpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyegggad
ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3vd3B (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) 
    >3vd3B (B:)
rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
lpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyegggad
ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3vd3C (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) 
    >3vd3C (C:)
rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
lpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyegggad
ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3vd3D (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) 
    >3vd3D (D:)
rrdwenpgvtqlnrlaahppfaswrnseeartdrpsqqlrslngewrfawfpapeavpes
wlecdlpeadtvvvpsnwqmhgydapiytnvtypitvnppfvptenptgcysltfnvdes
wlqegqtriifdgvnsafhlwcngrwvgygqdsrlpsefdlsaflragenrlavmvlrws
dgsyledqdmwrmsgifrdvsllhkpttqisdfhvatrfnddfsravleaevqmcgelrd
ylrvtvslwqgetqvasgtapfggeiiderggyadrvtlrlnvenpklwsaeipnlyrav
velhtadgtlieaeacdvgfrevriengllllngkpllirgvnrhehhplhgqvmdeqtm
vqdillmkqnnfnavrcshypnhplwytlcdryglyvvdeaniethgmvpmnrltddprw
lpamservtrmvqrdrnhpsviiwslgdesghganhdalyrwiksvdpsrpvqyegggad
ttatdiicpmyarvdedqpfpavpkwsikkwlslpgetrplilceyahamgnslggfaky
wqafrqyprlqggfvwdwvdqslikydengnpwsayggdfgdtpndrqfcmnglvfadrt
phpalteakhqqqffqfrlsgqtievtseylfrhsdnellhwmvaldgkplasgevpldv
apqgkqlielpelpqpesagqlwltvrvvqpnatawseaghisawqqwrlaenlsvtlpa
ashaiphlttsemdfcielgnkrwqfnrqsgflsqmwigdkkqlltplrdqftrapldnd
igvseatridpnawverwkaaghyqaeaallqctadtladavlittahawqhqgktlfis
rktyridgsgqmaitvdvevasdtphpariglncqlaqvaervnwlglgpqenypdrlta
acfdrwdlplsdmytpyvfpsenglrcgtrelnygphqwrgdfqfnisrysqqqlmetsh
rhllhaeegtwlnidgfhmgiggddswspsvsaefqlsagryhyqlvwcqk