Structure of PDB 8r56 Chain D Binding Site BS01

Receptor Information
>8r56 Chain D (length=673) Species: 592022 (Priestia megaterium DSM 319) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTKGVNVEILQDGFEVALNGVVLLQHTIQKPMLFVGHGEETIEMYRGNFD
IKDYVTERTALRYANVEEMEGAYKIDLSNLKNGDTMLSLIVKEEENRLKV
EYQKNDANINRFWLRVAADKQEKVYGCGEQLSHFNMRGKNFPLWTSEPGV
GRNKQTYVTWQADVVDKAGGDYYNTNFPQPTYVSSKKYYCHVETTAYADF
DFRNEAFHELQVWEVPKYMLFETADTYLELVEKITGLFGRQPELPEWVYN
GVVLGIQGGTDVVEQKLEKVLAKGMKVSGVWCQDWQGKRITSFGKRLMWN
WKWNESEYPELDKKIAEWKENDIRFLGYINPYVAIEGDLYKEAEDKGYLA
LNTEGNTYLVDFGEFYCGVVDFTNEEATEWYKQVIKENMIDFGLDGWMAD
FGEYLPTDVVLKNRIDAKIMHNAWPTMWAKVNYEAVSEAGKLGEIVYFMR
AGYTGIQKYCTLLWGGDQSVDWSLDDGLASVIPAALSSGMIGCGLHHSDI
GGYTSLHGNKRSKELLMRWAEMGAFTPMMRTHEGNRPDDCFQFDGDEETL
EHLARMSNVYVTMAPYIKSLVEENARRGIPVQRPLFMHYEEDEKTYDIQY
QYLFGEDVLVAPVHQENQTEWEVYLPEDQWVHVWSGEAYTGGSVTVQAPL
GYPPVFYRKKSIWSELFSKLIHI
Ligand information
Ligand IDY2W
InChIInChI=1S/C7H15NO6S/c8-4-1-5(9)7(11)6(10)3(4)2-15(12,13)14/h3-7,9-11H,1-2,8H2,(H,12,13,14)/t3-,4+,5-,6+,7+/m0/s1
InChIKeyUVCDOBMNOOKYMK-PJEQPVAWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O)CS(=O)(=O)O)N
CACTVS 3.385N[C@@H]1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1C[S](O)(=O)=O
OpenEye OEToolkits 2.0.7C1C(C(C(C(C1O)O)O)CS(=O)(=O)O)N
CACTVS 3.385N[CH]1C[CH](O)[CH](O)[CH](O)[CH]1C[S](O)(=O)=O
FormulaC7 H15 N O6 S
Name[(1~{S},2~{R},3~{R},4~{S},6~{R})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexyl]methanesulfonic acid
ChEMBL
DrugBank
ZINC
PDB chain8r56 Chain D 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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PDB8r56 Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes.
Resolution2.45 Å
Binding residue
(original residue number in PDB)
Q289 R302 L303 W305 Y334 M404 D406 F407 W470 D473 Y509 H538
Binding residue
(residue number reindexed from 1)
Q283 R296 L297 W299 Y328 M398 D400 F401 W464 D467 Y503 H532
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:8r56, PDBe:8r56, PDBj:8r56
PDBsum8r56
PubMed38647177
UniProtD5E1T0

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