Structure of PDB 5mko Chain B Binding Site BS01

Receptor Information
>5mko Chain B (length=302) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKCKFCSREAYIKIHYPKMYLCEEHFKEYFERKVSRTIERYKLLTKDER
ILVAVSGGKDSAVTAYVLKKLGYNIECLHINLGISGYSEKSEEYAKKQCK
LIGAPLHIVRIKEILGYGIGEVKTRRPPCSYCGLTKRYIMNKFAYDNGFD
AIATGHNLDDEASFLLNNILHWNTEYLAKGGPILPQQGKFIKKVKPLYEV
TEREVVAYALAVGLEYIVEECPYGATTLDMKGVLNELEEKRPGTKFNFVR
GYLKKKKLFEPEIKEKEIKECKICRMPSSGDICAFCKFWGLKKEINFKVS
ST
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 chain5mko Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mko Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		A53 V54 S55 S60 I79 K135 T153 G154 H155
Binding residue
(residue number reindexed from 1)		A54 V55 S56 S61 I80 K136 T154 G155 H156
Annotation score5
Enzymatic activity
Enzyme Commision number 2.8.1.-
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:5mko, PDBe:5mko, PDBj:5mko
PDBsum5mko
PubMed28655838
UniProtO58038|TTUA_PYRHO tRNA-5-methyluridine(54) 2-sulfurtransferase (Gene Name=ttuA)

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