Structure of PDB 7dkt Chain A Binding Site BS01

Receptor Information
>7dkt Chain A (length=769) Species: 858215 (Thermoanaerobacterium xylanolyticum LX-11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKISHKIDIPDSAWTIGIGEKFKNAGHPNVKYPMIDDSYVQGAPLGGFGA
GTIGRTYNGGFSRWHLEIGKNKYTTVYANQFSVFQKVEGNKDGVAQVLYA
GEPENGYLSSWKWDYPKESGMYYALYPNSWYTYTNKDLPVQLAVKQFSPI
IPYNYKETSYPVAVFKWTAYNPTNKNVDVSIMFTWQNMIGFFGKQVNVNS
GNFNKIIKDKSKDSEIVAAVMGNISNDNEEWNGEYSIGVKKVPGVDISYK
AKFVTTGDGSDLWHEFSKNGILDNKDDETPTKQDGIGSAIAVNFKLQPGQ
TIEVPFALSWDLPIMKFGGGDKWYKMYTKYFGKNGKNSFAILKEALNNYQ
KWEKMIDDWQKPILSNKSKPDWYKTALFNELYYLADGGTAWENGKVGEKR
TNNMFGLLACFDYNYYETLDVRFYGSFPLVMLWPDIEKQVMRQFADTINV
QDSSEFKVGSNGAMAVKKVQGMIPHDLGSSYALPWIKINAYDWQNPNIWK
DLNSKYVLLVYRDYVLTGKTDKEFLKYTWKSVKTALDKLKEMDKDNDGIP
DNEGIPDQTYDTWSMKGTSAYCGSLWLAALKAAQEIGKVLKDNEAYIKYN
EWYKIAQQNFEKELWNGEYYNFDTESDHKDSIMADQLAGQWYADILRLGD
ILPKDHVQKALKKIYEFNVMKFENGKMGAVNGMRPDGIVDESDIQAQEVW
TGVTYALASFMKYRGMTEEAYNTAYGVYKMTYDKSGKGYWFRTPEAWTKD
GNYRASMYMRPLSIWSMEV
Ligand information
Ligand IDGLF
InChIInChI=1S/C6H11FO5/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
InChIKeyATMYEINZLWEOQU-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)F)O)O)O)O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)F)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](F)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](F)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04FC1OC(C(O)C(O)C1O)CO
FormulaC6 H11 F O5
Namealpha-D-glucopyranosyl fluoride;
1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE;
alpha-D-glucosyl fluoride;
D-glucosyl fluoride;
glucosyl fluoride
ChEMBL
DrugBank
ZINCZINC000005131876
PDB chain7dkt Chain A Residue 1001 [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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PDB7dkt Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		Y445 D452 H507 Y523 T591 W732 E777 R786 Y790
Binding residue
(residue number reindexed from 1)		Y413 D420 H475 Y491 T559 W700 E745 R754 Y758
Annotation score2
Enzymatic activity
Enzyme Commision number 3.2.1.45: glucosylceramidase.
Gene Ontology
Molecular Function
GO:0004348 glucosylceramidase activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008422 beta-glucosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7dkt, PDBe:7dkt, PDBj:7dkt
PDBsum7dkt
PubMed34019851
UniProtF6BL85

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