Structure of PDB 4rdi Chain D Binding Site BS01

Receptor Information
>4rdi Chain D (length=239) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVISDAWRQRFGGTARLYGEKALQLFADAHICVVGIGGVGSWAAEALART
GIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMAERIRQINPECRV
TVVDDFVTPDNVAQYMSVGYSYVIDAIDSVRPKAALIAYCRRNKIPLVTT
GGAGGQIDPTQIQVTDLAKTIQDPLAAKLRERLKSDFGVVKNSKGKLGVD
CVFSTEALGFGAATMVTATFGFVAVSHALKKMMAKAARQ
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 chain4rdi Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4rdi 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.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		G37 G40 D61 R72 Q73 K85 F108 V109 I129 D130 P134
Binding residue
(residue number reindexed from 1)		G35 G38 D59 R70 Q71 K83 F106 V107 I127 D128 P132
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:4rdi, PDBe:4rdi, PDBj:4rdi
PDBsum4rdi
PubMed26101842
UniProtQ46927|TCDA_ECOLI tRNA threonylcarbamoyladenosine dehydratase (Gene Name=tcdA)

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