Structure of PDB 4ydu Chain C Binding Site BS01

Receptor Information
>4ydu Chain C (length=230) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSG
TSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQ
GAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVH
ERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQ
MFAEGKTVAVEHAEPVYLRNNVAWKKLPGK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4ydu Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ydu 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)		R32 H34 S67 I73
Binding residue
(residue number reindexed from 1)		R32 H34 S67 I73
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008237 metallopeptidase activity
GO:0042802 identical protein binding
Biological Process
GO:0002949 tRNA threonylcarbamoyladenosine modification
GO:0008033 tRNA processing
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
UniProtP76256|TSAB_ECOLI tRNA threonylcarbamoyladenosine biosynthesis protein TsaB (Gene Name=tsaB)

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