Structure of PDB 5a6k Chain B Binding Site BS01

Receptor Information
>5a6k Chain B (length=625) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRFTGLSLKQTQAIEVLKGHISLPDVEVAVTQSDQASISIEGEEGHYQLT
YRKPHQLYRALSLLVTVLAEADKVEIEEQAAYEDLAYMVDCSRNAVLNVA
SAKQMIEILALMGYSTFELYMEDTYQIEGQPYFGYFRGAYSAEELQEIEA
YAQQFDVTFVPCIQTLAHLSAFVKWGVKEVQELRDVEDILLIGEEKVYDL
IDGMFATLSKLKTRKVNIGMDEAHLVGLGRYLILNGVVDRSLLMCQHLER
VLDIADKYGFHCQMWSDMFFKLMSADGQYDRDVEIPEETRVYLDRLKDRV
TLVYWDYYQDSEEKYNRNFRNHHKISHDLAFAGGAWKWIGFTPHNHFSRL
VAIEANKACRANQIKEVIVTGWGDNGGETAQFSILPSLQIWAELSYRNDL
DGLSAHFKTNTGLTVEDFMQIDLANLLPDLPGNLSGINPNRYVFYQDILC
PILDQHMTPEQDKPHFAQAAETLANIKEKAGNYAYLFETQAQLNAILSSK
VDVGRRIRQAYQADDKESLQQIARQELPELRSQIEDFHALFSHQWLKENK
VFGLDTVDIRMGGLLQRIKRAESRIEVYLAGQLDRIDELEVEILPFTDFY
ADKDFAATTANQWHTIATASTIYTT
Ligand information
Ligand IDNSG
InChIInChI=1S/C8H15NO4S/c1-3-9-5-7(12)6(11)4(2-10)13-8(5)14-3/h3-12H,2H2,1H3/t3-,4+,5+,6-,7+,8+/m0/s1
InChIKeyXWPUWEBFKDEDIF-JMHNFOGYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1NC2C(C(C(OC2S1)CO)O)O
CACTVS 3.385C[CH]1N[CH]2[CH](O)[CH](O)[CH](CO)O[CH]2S1
CACTVS 3.385C[C@H]1N[C@@H]2[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]2S1
OpenEye OEToolkits 1.7.6C[C@H]1N[C@@H]2[C@H]([C@H]([C@H](O[C@@H]2S1)CO)O)O
FormulaC8 H15 N O4 S
Name(2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol
ChEMBL
DrugBank
ZINCZINC000199600282
PDB chain5a6k Chain B Residue 1627 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5a6k A Second Beta-Hexosaminidase Encoded in the Streptococcus Pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R94 D222 E223 W266 W306 Y308 W339 W373 D375
Binding residue
(residue number reindexed from 1)		R93 D221 E222 W265 W305 Y307 W338 W372 D374
Annotation score1
Binding affinityMOAD: Ki=1130nM
PDBbind-CN: -logKd/Ki=5.95,Ki=1130nM
Enzymatic activity
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0015929 hexosaminidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5a6k, PDBe:5a6k, PDBj:5a6k
PDBsum5a6k
PubMed26491009
UniProtA0A0H2US73

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