Structure of PDB 4kr7 Chain B Binding Site BS03

Receptor Information
>4kr7 Chain B (length=386) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELRVYIVRYSEIGLKGKNRKDFEEALRRNIERVTGMKVKRQWGRFLIPID
ENVTLDDKLKKIFGIQNFSKGFLVSHDFEEVKKYSLIAVKEKLEKGNYRT
FKVQAKKAYKEYKKGVYEINSELGALILKNFKELSVDVRNPDFVLGVEVR
PEGVLIFTDRVECYGGLPVGTGGKAVLLLSGGIDSPVAGWYALKRGVLIE
SVTFVSPPFTSEGAVEKVRDILRVLREFSGGHPLRLHIVNLTKLQLEVKK
RVPDKYSLIMYRRSMFRIAEKIAEETGAVAFYTGENIGQVASQTLENLWS
IESVTTRPVIRPLSGFDKTEIVEKAKEIGTYEISIKPYQDSCVFFAPKNP
ATRSHPSILEKLEQQVPDLPVLEEEAFTSRKVEVIE
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 chain4kr7 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4kr7 Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.
Resolution3.421 Å
Binding residue
(original residue number in PDB)		L180 L181 S182 D186 S187 T205 F206 R264 M267 G286
Binding residue
(residue number reindexed from 1)		L178 L179 S180 D184 S185 T203 F204 R262 M265 G284
Annotation score5
Enzymatic activity
Enzyme Commision number 2.8.1.4: tRNA uracil 4-sulfurtransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0004810 CCA tRNA nucleotidyltransferase activity
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0016783 sulfurtransferase activity
GO:0140741 tRNA-uracil-4 sulfurtransferase activity
Biological Process
GO:0002937 tRNA 4-thiouridine biosynthesis
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
GO:0034227 tRNA thio-modification
GO:0052837 thiazole biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4kr7, PDBe:4kr7, PDBj:4kr7
PDBsum4kr7
PubMed24705700
UniProtQ9X220|THII_THEMA Probable tRNA sulfurtransferase (Gene Name=thiI)

[Back to BioLiP]