Structure of PDB 4ydu Chain D Binding Site BS01

Receptor Information
>4ydu Chain D (length=229) 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
MFAEGKTVAVEHAEPVYLRNNVAWKKLPG
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 D 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 T69 I73 R118
Binding residue
(residue number reindexed from 1)		R32 H34 S67 T69 I73 R118
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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