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BioLiP

Structure of PDB 5jud Chain A Binding Site BS01

Receptor Information
>5jud Chain A (length=277) Species: 233413 (Mycobacterium tuberculosis variant bovis AF2122/97) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVD
GLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWR
SLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRGRVT
ELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLI
DTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSG
VGLTQFLYTRHTWPVSLVDRPPMKVMR
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 chain5jud 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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PDB5jud Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		P50 A51 L52 E54 S81 G113 K114 S135 D136 Y229
Binding residue
(residue number reindexed from 1)		P30 A31 L32 E34 S61 G93 K94 S115 D116 Y192
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.266: glucosyl-3-phosphoglycerate synthase.
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5jud, PDBe:5jud, PDBj:5jud
PDBsum5jud
PubMed28625787
UniProtQ7U0E1|GPGS_MYCBO Glucosyl-3-phosphoglycerate synthase (Gene Name=gpgS)

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