PDB entry 6ldc

View 6ldc on RCSB PDB site
Description: structure of bifidobacterium dentium beta-glucuronidase complexed with c6-nonyl uronic isofagomine
Deposited on 2019-11-20, released 2021-01-27
The last revision was dated 2021-08-11, with a file datestamp of 2021-08-06.
Experiment type: XRAY
Resolution: 2.18 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: LacZ1 Beta-galactosidase
    Species: Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) [TaxId:401473]
    Gene: lacZ1, BDP_2112
    Database cross-references and differences (RAF-indexed):
    • Uniprot D2Q7B1 (2-669)
      • expression tag (0-1)
  • Chain 'B':
    Compound: LacZ1 Beta-galactosidase
    Species: Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) [TaxId:401473]
    Gene: lacZ1, BDP_2112
    Database cross-references and differences (RAF-indexed):
    • Uniprot D2Q7B1 (2-669)
      • expression tag (0-1)
  • Chain 'C':
    Compound: LacZ1 Beta-galactosidase
    Species: Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) [TaxId:401473]
    Gene: lacZ1, BDP_2112
    Database cross-references and differences (RAF-indexed):
    • Uniprot D2Q7B1 (2-669)
      • expression tag (0-1)
  • Chain 'D':
    Compound: LacZ1 Beta-galactosidase
    Species: Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) [TaxId:401473]
    Gene: lacZ1, BDP_2112
    Database cross-references and differences (RAF-indexed):
    • Uniprot D2Q7B1 (2-669)
      • expression tag (0-1)
  • Heterogens: E9O, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6ldcA (A:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsdnanvpavaeakkharrqnlpnf
dffnfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdfps
nptdpntpiqpsdpainhadssesaesdiqrattygrqvrisildgegtvvagvtadier
sgdgtakasgeiairdaklwnpgaaylytavaellpeggaesssriidayrqtfgirtve
vsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfrtshypyae
smydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpcivmwsian
epgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditertmdvvcinr
yygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgemfseefqrd
yyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkmaahwlrerw
agipdygykg

    Sequence, based on observed residues (ATOM records):
    >6ldcA (A:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsnvpavaeakkharrqnlpnfdff
nfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdgrqvri
sildgegtvvagvtadiertakasgeiairdaklwnpgaaylytavaellpsriidayrq
tfgirtvevsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfr
tshypyaesmydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpc
ivmwsianepgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditert
mdvvcinryygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgem
fseefqrdyyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkma
ahwlrerwagipdygyk

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6ldcB (B:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsdnanvpavaeakkharrqnlpnf
dffnfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdfps
nptdpntpiqpsdpainhadssesaesdiqrattygrqvrisildgegtvvagvtadier
sgdgtakasgeiairdaklwnpgaaylytavaellpeggaesssriidayrqtfgirtve
vsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfrtshypyae
smydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpcivmwsian
epgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditertmdvvcinr
yygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgemfseefqrd
yyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkmaahwlrerw
agipdygykg

    Sequence, based on observed residues (ATOM records):
    >6ldcB (B:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsnvpavaeakkharrqnlpnfdff
nfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdgrqvri
sildgegtvvagvtadiertakasgeiairdaklwnpgaaylytavaellpsriidayrq
tfgirtvevsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfr
tshypyaesmydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpc
ivmwsianepgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditert
mdvvcinryygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgem
fseefqrdyyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkma
ahwlrerwagipdygyk

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6ldcC (C:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsdnanvpavaeakkharrqnlpnf
dffnfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdfps
nptdpntpiqpsdpainhadssesaesdiqrattygrqvrisildgegtvvagvtadier
sgdgtakasgeiairdaklwnpgaaylytavaellpeggaesssriidayrqtfgirtve
vsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfrtshypyae
smydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpcivmwsian
epgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditertmdvvcinr
yygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgemfseefqrd
yyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkmaahwlrerw
agipdygykg

    Sequence, based on observed residues (ATOM records):
    >6ldcC (C:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsnvpavaeakkharrqnlpnfdff
nfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdgrqvri
sildgegtvvagvtadiertakasgeiairdaklwnpgaaylytavaellpsriidayrq
tfgirtvevsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfr
tshypyaesmydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpc
ivmwsianepgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditert
mdvvcinryygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgem
fseefqrdyyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkma
ahwlrerwagipdygyk

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6ldcD (D:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsdnanvpavaeakkharrqnlpnf
dffnfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdfps
nptdpntpiqpsdpainhadssesaesdiqrattygrqvrisildgegtvvagvtadier
sgdgtakasgeiairdaklwnpgaaylytavaellpeggaesssriidayrqtfgirtve
vsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfrtshypyae
smydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpcivmwsian
epgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditertmdvvcinr
yygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgemfseefqrd
yyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkmaahwlrerw
agipdygykg

    Sequence, based on observed residues (ATOM records):
    >6ldcD (D:)
ngmlypqsndsrivfpldgvwdfrtagedsypaewadaplpeplpmavpgsyndqndeln
lrahygwvvyqrsfavpsrlvagqrmilrfdaathaadvylngqllgshfggflpfefdv
tsalhagenlltvavdnrigsstlpvgndagtafmgsnvpavaeakkharrqnlpnfdff
nfaglnrhvelyttpadayiadiaitterldhiagdactaanaliaydvtfggdgrqvri
sildgegtvvagvtadiertakasgeiairdaklwnpgaaylytavaellpsriidayrq
tfgirtvevsgttflingkpfyfkgfgkhedsyfhgrgtddvlnvkdvslihwlhansfr
tshypyaesmydlcdregiviidevpavgmswlqyanplvaerhreairgmiardknhpc
ivmwsianepgldgdgerprqaydyfrplyelahasdpqnrpvtlvccqndyttditert
mdvvcinryygwynlsgdldaachalnieldfwenigkpvmfteygadtiegihgthgem
fseefqrdyyarinaeidkrpwfigeqlwnfadfatfqgiirvegnrkgiltrdrqpkma
ahwlrerwagipdygyk