Structure of PDB 5bxs Chain A Binding Site BS01

Receptor Information
>5bxs Chain A (length=633) Species: 398514 (Bifidobacterium bifidum JCM 1254) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVS
SDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDE
GFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKY
KERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKA
ATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADN
SGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFD
NYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVN
TKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKV
NAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEK
EIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAG
IYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQ
VGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQ
RLAIATGNEQNIDLETHRPAAGTVAQFPADLVS
Ligand information
Ligand IDGAL
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
InChIKeyWQZGKKKJIJFFOK-FPRJBGLDSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O
OpenEye OEToolkits 1.7.2C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.370OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01OC1C(O)C(OC(O)C1O)CO
OpenEye OEToolkits 1.7.2C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
FormulaC6 H12 O6
Namebeta-D-galactopyranose;
beta-D-galactose;
D-galactose;
galactose
ChEMBLCHEMBL300520
DrugBank
ZINCZINC000002597049
PDB chain5bxs Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5bxs Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis
Resolution2.2 Å
Binding residue
(original residue number in PDB)		C189 E216 N259 H263 D320 P466 D467
Binding residue
(residue number reindexed from 1)		C160 E187 N230 H234 D291 P437 D438
Annotation score3
Enzymatic activity
Enzyme Commision number 3.2.1.140: lacto-N-biosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5bxs, PDBe:5bxs, PDBj:5bxs
PDBsum5bxs
PubMed26312778
UniProtB3TLD6|LNBB_BIFB1 Lacto-N-biosidase (Gene Name=lnbB)

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