Structure of PDB 3pkp Chain K Binding Site BS01

Receptor Information
>3pkp Chain K (length=284) 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]
KTRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRD
ILIISTPQDTPRFQQLLGDGSQWGLNLQYKVSPSPDGLAQAFIIGEEFIG
HDDCALVLGDNIFYGHDLPKLMEAAVATVFAYHVNDPERYGVVEFDQKGT
AVSLEEKPLQPKSNYAVTGLYFYDNSVVEMAKNLKPSARGELEITDINRI
YMEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEE
IAFRKNFINAQQVIELAGPLSKNDYGKYLLKMVK
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[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(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain3pkp Chain K 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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PDB3pkp Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G11 G12 S13 G14 T15 R16 K26 Q27 S83 P86 G110 D111
Binding residue
(residue number reindexed from 1)		G10 G11 S12 G13 T14 R15 K25 Q26 S82 P85 G109 D110
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:3pkp, PDBe:3pkp, PDBj:3pkp
PDBsum3pkp
PubMed21317292
UniProtP26393|RMLA_SALTY Glucose-1-phosphate thymidylyltransferase (Gene Name=rmlA)

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