Structure of PDB 4yed Chain A Binding Site BS01

Receptor Information
>4yed Chain A (length=245) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVVISDAWRQRFGGTARLYGEKALQLFADAHICVVGIGGVGSWAAEALAR
TGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMAERIRQINPECR
VTVVDDFVTPDNVAQYMSVGYSYVIDAIDSVRPKAALIAYCRRNKIPLVT
TGGAGGQIDPTQIQVTDLAKTIQDPLAAKLRERLKSDFGVVKNSKGKLGV
DCVFSTEALVYPQSGFGAATMVTATFGFVAVSHALKKMMAKAARQ
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain4yed Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yed The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G37 G39 G40 I60 D61 D63 R72 K85 F108 V109 I129 D130 P134
Binding residue
(residue number reindexed from 1)		G36 G38 G39 I59 D60 D62 R71 K84 F107 V108 I128 D129 P133
Annotation score4
Enzymatic activity
Enzyme Commision number 6.1.-.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016874 ligase activity
GO:0030955 potassium ion binding
GO:0031402 sodium ion binding
GO:0042803 protein homodimerization activity
GO:0061503 tRNA threonylcarbamoyladenosine dehydratase
Biological Process
GO:0061504 cyclic threonylcarbamoyladenosine biosynthetic process
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yed, PDBe:4yed, PDBj:4yed
PDBsum4yed
PubMed26101842
UniProtQ46927|TCDA_ECOLI tRNA threonylcarbamoyladenosine dehydratase (Gene Name=tcdA)

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