Structure of PDB 4wq5 Chain B Binding Site BS03

Receptor Information
>4wq5 Chain B (length=336) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRD
HVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLEGALLVGATVGRSLAF
AWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQ
YELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRP
MTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIK
CKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTD
NGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[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
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4wq5 Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4wq5 The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		M112 H115 S136 G137 G138 H139 G163 F166 D167 G180 P181 G268 N272 D300
Binding residue
(residue number reindexed from 1)		M112 H115 S136 G137 G138 H139 G163 F166 D167 G180 P181 G268 N272 D300
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.1.234: N(6)-L-threonylcarbamoyladenine synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0061711 N(6)-L-threonylcarbamoyladenine synthase activity
GO:0140032 glycosylation-dependent protein binding
Biological Process
GO:0002949 tRNA threonylcarbamoyladenosine modification
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0070525 tRNA threonylcarbamoyladenosine metabolic process
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0000408 EKC/KEOPS complex
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:4wq5, PDBe:4wq5, PDBj:4wq5
PDBsum4wq5
PubMed25578970
UniProtP05852|TSAD_ECOLI tRNA N6-adenosine threonylcarbamoyltransferase (Gene Name=tsaD)

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