Structure of PDB 7vm0 Chain A Binding Site BS01

Receptor Information
>7vm0 Chain A (length=386) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANVLMIGFPGEGHINPSIGVMKELKSRGENITYYAVKEYKEKITALDIEF
REYHDFRGFGKNATGDEERDFTEMLCAFLKACKDIATHIYEEVKHESYDY
VIYDHHLLAGKVIANMLKLPRFSLCTTFAMNEEFEDSPHYESYQQLAETL
NADFQAEIKKPFDVFLADGDLTIVFTSRGFQPLAEQFGERYVFVGPSITE
RADFPFDQIDNENVLFISMGTIFNNQKQFFNQCLEVCKDFDGKVVLSIGK
HIKTSELNDIPENFIVRPYVPQLEILKRASLFVTHGGMNSTSEGLYFETP
LVVIPMGGDQFVVADQVEKVGAGKVIKKEELSESLLKETIQEVMNNRSYA
EKAKEIGQSLKAAGGSKKAADSILEAVKQKTQSANA
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain7vm0 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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PDB7vm0 Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E12 N16 R217 T240 S266 Y288 V289 Q291 H304 G306 N308 S309 E312
Binding residue
(residue number reindexed from 1)		E11 N15 R201 T221 S247 Y269 V270 Q272 H285 G287 N289 S290 E293
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.-
Gene Ontology
Molecular Function
GO:0008194 UDP-glycosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0009058 biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7vm0, PDBe:7vm0, PDBj:7vm0
PDBsum7vm0
PubMed36091437
UniProtO31853|YOJK_BACSU Uncharacterized UDP-glucosyltransferase YojK (Gene Name=yojK)

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