Structure of PDB 5b4e Chain A Binding Site BS03

Receptor Information
>5b4e Chain A (length=303) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VCKVCGQKAQVEMRSRGLALCREHYLDWFVKETERAIRRHRMLLPGERVL
VAVSGGKDSLALWDVLSRLGYQAVGLHIELGIGEYSKRSLEVTQAFARER
GLELLVVDLKEAYGFGVPELARLSGRVACSACGLSKRYIINQVAVEEGFR
VVATGHNLDDEAAVLFGNLLNPQEQGPVLPEKPGLAARVKPFYRFSEREV
LSYTLLRGIRYLHEECPNAKGAKSLLYKEALNLVERSMPGAKLRFLDGFL
EKIVALRECERCGYPTTGAVCAFCRMWDAVYRRAKKRKLLPEEVSFRPRV
KPL
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5b4e Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5b4e Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA
Resolution2.698 Å
Binding residue
(original residue number in PDB)		A53 V54 S55 G57 D59 S60 I79 G156 H157
Binding residue
(residue number reindexed from 1)		A52 V53 S54 G56 D58 S59 I78 G155 H156
Annotation score3
Enzymatic activity
Enzyme Commision number 2.8.1.15: tRNA-5-methyluridine(54) 2-sulfurtransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0002143 tRNA wobble position uridine thiolation
GO:0008033 tRNA processing
GO:0034227 tRNA thio-modification
Cellular Component
GO:0002144 cytosolic tRNA wobble base thiouridylase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5b4e, PDBe:5b4e, PDBj:5b4e
PDBsum5b4e
PubMed28439027
UniProtQ72LF3|TTUA_THET2 tRNA-5-methyluridine(54) 2-sulfurtransferase (Gene Name=ttuA)

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