Structure of PDB 4ydu Chain A

Receptor sequence
>4yduA (length=336) Species: 562 (Escherichia coli) [Search protein sequence]
MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRD
HVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAF
AWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQ
YELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRP
MTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIK
CKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTD
NGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPA
3D structure
PDB4ydu The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.
ChainA
Resolution2.33 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.3.1.234: N(6)-L-threonylcarbamoyladenine synthase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ADP A H111 H115 S136 G137 G163 F166 D167 G268 N272 T299 D300 H111 H115 S136 G137 G163 F166 D167 G268 N272 T299 D300
BS02 MG A D11 E12 D11 E12
BS03 FE A H111 H115 D300 H111 H115 D300
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:4ydu, PDBe:4ydu, PDBj:4ydu
PDBsum4ydu
PubMed25578970
UniProtP05852|TSAD_ECOLI tRNA N6-adenosine threonylcarbamoyltransferase (Gene Name=tsaD)

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