Structure of PDB 4cu8 Chain A Binding Site BS01

Receptor Information
>4cu8 Chain A (length=848) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVTNEEVNQMIEDRKVDFNQNWYFKLNANSKEAIKPDADVSTWKKLDLPY
DWSIFNDFDHESPAQNEGGQLNGGEAWYRKTFKLDEKDLKKNVRLTFDGV
YMDSQVYVNGQLVGHYPNGYNQFSYDITKYLQKDGRENVIAVHAVNKQPS
SRWYSGSGIYRDVTLQVTDKVHVEKNGTTILTPKLEEQQHGKVETHVTSK
IVNTDDKDHELVAEYQIVERGGHAVTGLVRTASRTLKAHESTSLDAILEV
ERPKLWTVLNDKPALYELITRVYRDGQLVDAKKDLFGYRYYHWTPNEGFS
LNGERIKFHGVSLHHDHGALGAEENYKAEYRRLKQMKEMGVNSIRTTHNP
ASEQTLQIAAELGLLVQEEAFDTWYGGKKPYDYGRFFEKDATHPEARKGE
KWSDFDLRTMVERGKNNPAIFMWSIGNEIGEANGDAHSLATVKRLVKVIK
DVDKTRYVTMGADKFRFGNGSGGHEKIADELDAVGFNYSEDNYKALRAKH
PKWLIYGSETSSATRTRGSYYRPERELKHSNGPERNYEQSDYGNDRVGWG
KTATASWTFDRDNAGYAGQFIWTGTDYIGEPTPWHNQNQTPVKSSYFGIV
DTAGIPKHDFYLYQSQWVSVKKKPMVHLLPHWNWENKELASKVADSEGKI
PVRAYSNASSVELFLNGKSLGLKTFNKKQTSDGRTYQEGANANELYLEWK
VAYQPGTLEAIARDESGKEIARDKITTAGKPAAVRLIKEDHAIAADGKDL
TYIYYEIVDSQGNVVPTANNLVRFQLHGQGQLVGVDNGEQASRERYKAQA
DGSWIRKAFNGKGVAIVKSTEQAGKFTLTAHSDLLKSNQVTVFTGKKE
Ligand information
Ligand IDDGJ
InChIInChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5+,6-/m1/s1
InChIKeyLXBIFEVIBLOUGU-DPYQTVNSSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OC1C(NCC(O)C1O)CO
OpenEye OEToolkits 1.7.2C1C(C(C(C(N1)CO)O)O)O
OpenEye OEToolkits 1.7.2C1[C@@H]([C@H]([C@H]([C@H](N1)CO)O)O)O
CACTVS 3.370OC[CH]1NC[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1NC[C@H](O)[C@@H](O)[C@H]1O
FormulaC6 H13 N O4
Name(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol;
1-deoxygalactonojirimycin
ChEMBLCHEMBL110458
DrugBankDB05018
ZINCZINC000001636704
PDB chain4cu8 Chain A Residue 1985 [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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PDB4cu8 Unravelling the Multiple Functions of the Architecturally Intricate Streptococcus Pneumoniae Beta-Galactosidase, Bgaa.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		R288 H484 N563 E564 E645 S648 W685 W708 E716 F733
Binding residue
(residue number reindexed from 1)		R152 H348 N427 E428 E509 S512 W549 W572 E580 F597
Annotation score1
Binding affinityMOAD: Ki=33.9uM
PDBbind-CN: -logKd/Ki=4.47,Ki=33.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) R288 H450 H484 T509 Y511 E564 Y629 E645 S730 F733
Catalytic site (residue number reindexed from 1) R152 H314 H348 T373 Y375 E428 Y493 E509 S594 F597
Enzyme Commision number 3.2.1.23: beta-galactosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4cu8, PDBe:4cu8, PDBj:4cu8
PDBsum4cu8
PubMed25210925
UniProtA0A0H2UP19

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