Structure of PDB 4y6n Chain A Binding Site BS02

Receptor Information
>4y6n Chain A (length=282) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPL
VDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEAL
WRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRTG
GGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVE
IGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCG
IPDSGVGLTQFLYTRHTWPVSLVDRPPMKVMR
Ligand information
Ligand IDUPG
InChIInChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
InChIKeyHSCJRCZFDFQWRP-JZMIEXBBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
CACTVS 3.370OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
FormulaC15 H24 N2 O17 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCOSE;
URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
ChEMBLCHEMBL375951
DrugBankDB01861
ZINCZINC000008215472
PDB chain4y6n Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4y6n A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase.
Resolution2.348 Å
Binding residue
(original residue number in PDB)		A51 L52 E54 S81 G113 K114 D134 S135 D136 L209 Y229 E232 H258 R259 R261 M269
Binding residue
(residue number reindexed from 1)		A33 L34 E36 S63 G95 K96 D116 S117 D118 L177 Y197 E200 H226 R227 R229 M237
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.266: glucosyl-3-phosphoglycerate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006011 UDP-glucose metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4y6n, PDBe:4y6n, PDBj:4y6n
PDBsum4y6n
PubMed26136334
UniProtP9WMW9|GPGS_MYCTU Glucosyl-3-phosphoglycerate synthase (Gene Name=gpgS)

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