Structure of PDB 3pkq Chain D Binding Site BS01

Receptor Information
>3pkq Chain D (length=278) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDIL
IISTPQDTPRFQQLLGDGSQWGLNLQYKVDPSPDGLAQAFIIGEEFIGHD
DCALVLGDNIFYGHDLPKLMEAAVNKSGATVFAYHVNDPERYGVVEFDGT
AVSLEEKPPKSNYAVTGLYFYDNSVVEMAKNLKPSLEITDINRIYMEQGR
LSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKN
FINAQQVIELAGPLSKNDYGKYLLKMVK
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain3pkq Chain D Residue 500 [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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PDB3pkq Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		L9 G11 G12 S13 G14 T15 R16 Q27 D83 S85 L109 G110 D111
Binding residue
(residue number reindexed from 1)		L6 G8 G9 S10 G11 T12 R13 Q24 D80 S82 L106 G107 D108
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.7.24: glucose-1-phosphate thymidylyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008879 glucose-1-phosphate thymidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pkq, PDBe:3pkq, PDBj:3pkq
PDBsum3pkq
PubMed21317292
UniProtP26393|RMLA_SALTY Glucose-1-phosphate thymidylyltransferase (Gene Name=rmlA)

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