Structure of PDB 5bxp Chain A Binding Site BS01

Receptor Information
>5bxp Chain A (length=636) Species: 398514 (Bifidobacterium bifidum JCM 1254) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHSSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRV
VSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELG
DEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKP
KYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTK
KAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLA
DNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTS
FDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGI
VNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVY
KVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEV
EKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVD
AGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVV
TQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALT
QQRLAIATGNEQNIDLETHRPAAGTVAQFPADLVSD
Ligand information
Ligand IDLOG
InChIInChI=1S/C8H14N2O6/c1-3(12)9-5-7(14)6(13)4(2-11)16-8(5)10-15/h4-7,11,13-15H,2H2,1H3,(H,9,12)/b10-8-/t4-,5-,6-,7-/m1/s1
InChIKeyNJBKCLCEXIDHDR-OANDGCGGSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NO
ACDLabs 10.04O=C(NC1C(=N\O)\OC(CO)C(O)C1O)C
OpenEye OEToolkits 1.6.1CC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\O)CO)O)O
CACTVS 3.352CC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\O
OpenEye OEToolkits 1.6.1CC(=O)NC1C(C(C(OC1=NO)CO)O)O
FormulaC8 H14 N2 O6
NameN-acetylglucosaminono-1,5-lactone (Z)-oxime;
LOGNAC
ChEMBLCHEMBL402605
DrugBank
ZINCZINC000005167376
PDB chain5bxp Chain C Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5bxp Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis
Resolution1.7 Å
Binding residue
(original residue number in PDB)		D320 E321 W394 Y419 Y427 W465 D467
Binding residue
(residue number reindexed from 1)		D293 E294 W367 Y392 Y400 W438 D440
Annotation score2
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:5bxp, PDBe:5bxp, PDBj:5bxp
PDBsum5bxp
PubMed26312778
UniProtB3TLD6|LNBB_BIFB1 Lacto-N-biosidase (Gene Name=lnbB)

[Back to BioLiP]