Structure of PDB 3ek5 Chain A Binding Site BS01

Receptor Information
>3ek5 Chain A (length=241) Species: 340 (Xanthomonas campestris pv. campestris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAMSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQV
ALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAK
VRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAAL
RAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMD
TAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGR
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain3ek5 Chain E Residue 2004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ek5 Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium
Resolution2.56 Å
Binding residue
(original residue number in PDB)		R100 N108 D109 V110 C111 E112 R118 R127
Binding residue
(residue number reindexed from 1)		R102 N110 D111 V112 C113 E114 R120 R129
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.22: UMP kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0033862 UMP kinase activity
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0044210 'de novo' CTP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ek5, PDBe:3ek5, PDBj:3ek5
PDBsum3ek5
PubMed19059268
UniProtP59009|PYRH_XANCP Uridylate kinase (Gene Name=pyrH)

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