Structure of PDB 4f79 Chain A Binding Site BS01

Receptor Information
>4f79 Chain A (length=478) Species: 1309 (Streptococcus mutans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMSKLPENFLWGGAVAAHQLEGGWQEGGKGISVADVMTAGRHGVAREITA
GVLEGKYYPNHEAIDFYHHYKEDVKLFAEMGFKCFRTSIAWTRIFPKGDE
AEPNEAGLQFYDDLFDECLKYGIEPVVTLSHFELPYHLVTEYGGFTNRKV
IDFFVHFAEVCFRRYKDKVKYWMTFNEINNQANYQEDFAPFTNSGIVYKE
GDDREAIMYQAAHYELVASARAVKIGHAINPNLNIGCMVAMCPIYPATCN
PKDILMAQKAMQKRYYFADVHVHGFYPEHIFKYWERKAIKVDFTERDKKD
LFEGTVDYIGFSYYMSFVIDAHRENNPYYDYLETEDLVKNPYVKASDWDW
QIDPQGLRYALNWFTDMYHLPLFIVQNGFGAIDQVEADGMVHDDYRIDYL
GAHIKEMIKAVDEDGVELMGYTPWGCIDLVSAGTGEMRKRYGFIYVDKDD
EGKGTLKRSPKLSFNWYKEVIASNGDDI
Ligand information
Ligand IDP53
InChIInChI=1S/C13H19O10P/c14-5-7-3-1-2-4-8(7)22-13-12(17)11(16)10(15)9(23-13)6-21-24(18,19)20/h1-4,9-17H,5-6H2,(H2,18,19,20)/t9-,10-,11+,12-,13-/m1/s1
InChIKeyFSJKOMDYZYBBLV-UJPOAAIJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(c(c1)CO)OC2C(C(C(C(O2)COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6c1ccc(c(c1)CO)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)O
CACTVS 3.370OCc1ccccc1O[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]2O
CACTVS 3.370OCc1ccccc1O[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H]2O
ACDLabs 12.01O=P(O)(O)OCC2OC(Oc1c(cccc1)CO)C(O)C(O)C2O
FormulaC13 H19 O10 P
Name2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucopyranoside;
Salicin-6-phosphate;
2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucoside;
2-(hydroxymethyl)phenyl 6-O-phosphono-D-glucoside;
2-(hydroxymethyl)phenyl 6-O-phosphono-glucoside
ChEMBL
DrugBank
ZINCZINC000004097049
PDB chain4f79 Chain A Residue 501 [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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PDB4f79 GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
Resolution2.54 Å
Binding residue
(original residue number in PDB)
Q18 H130 F131 E176 Y313 W349 Q375 W423 S430 A431 G432 K438 Y440
Binding residue
(residue number reindexed from 1)
Q19 H131 F132 E177 Y314 W350 Q376 W424 S431 A432 G433 K439 Y441
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R85 H130 E176 N179 S311 Y313 Q375
Catalytic site (residue number reindexed from 1) R86 H131 E177 N180 S312 Y314 Q376
Enzyme Commision number 3.2.1.86: 6-phospho-beta-glucosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008422 beta-glucosidase activity
GO:0008706 6-phospho-beta-glucosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0016052 carbohydrate catabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4f79, PDBe:4f79, PDBj:4f79
PDBsum4f79
PubMed23519420
UniProtQ8DT00

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