Structure of PDB 6kqx Chain A Binding Site BS01

Receptor Information
>6kqx Chain A (length=327) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HISMINIPAYGHVNPTLALVEKLCEKGHRVTYATTEEFAPAVQQAGGEAL
IYHTSLNESLSILPQLEELYKDDQPDLIIYDFVALAGKLFAEKLNVPVIK
LCSSYAQNESFQLGNEDMLKQLAVPEALNIVFMPKSFQIQHETFDDRFCF
VGPSLGIDKDDRPLMLISLGTAFNAWPEFYKMCIKAFRDSSWQVIMSVGK
TIDPESLEDIPANFTIRQSVPQLEVLEKADLFISHGGMNSTMEAMNAGVP
LVVIPQMYEQELTANRVDELGLGVYLPKEEVTVSSLQEAVQAVSSDQELL
SRVKNMQKDVKEAGGAERAAAEIEAFM
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 chain6kqx Chain A Residue 401 [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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PDB6kqx Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity.
Resolution2.44 Å
Binding residue
(original residue number in PDB)		N18 G228 T229 S255 S277 V278 Q280 H293 G295 N297 S298 E301
Binding residue
(residue number reindexed from 1)		N14 G170 T171 S197 S219 V220 Q222 H235 G237 N239 S240 E243
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.384: NDP-glycosyltransferase.
Gene Ontology
Molecular Function
GO:0008194 UDP-glycosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6kqx, PDBe:6kqx, PDBj:6kqx
PDBsum6kqx
PubMed33310191
UniProtO34539|NDPGT_BACSU NDP-glycosyltransferase YjiC (Gene Name=yjiC)

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