Structure of PDB 5mko Chain B Binding Site BS04

Receptor Information

>5mko Chain B (length=302) Species: 70601 (Pyrococcus horikoshii OT3)

SMKCKFCSREAYIKIHYPKMYLCEEHFKEYFERKVSRTIERYKLLTKDER
ILVAVSGGKDSAVTAYVLKKLGYNIECLHINLGISGYSEKSEEYAKKQCK
LIGAPLHIVRIKEILGYGIGEVKTRRPPCSYCGLTKRYIMNKFAYDNGFD
AIATGHNLDDEASFLLNNILHWNTEYLAKGGPILPQQGKFIKKVKPLYEV
TEREVVAYALAVGLEYIVEECPYGATTLDMKGVLNELEEKRPGTKFNFVR
GYLKKKKLFEPEIKEKEIKECKICRMPSSGDICAFCKFWGLKKEINFKVS
ST

Ligand information

• Ligand ID: FES
• InChI: InChI=1S/2Fe.2S
• InChIKey: NIXDOXVAJZFRNF-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: [Fe]1S[Fe]S1
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: S1[Fe]S[Fe]1
• Formula: Fe2 S2
• Name: FE2/S2 (INORGANIC) CLUSTER
• PDB chain: 5mko Chain B Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mko Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): C128 C131 C220
• Binding residue (residue number reindexed from 1): C129 C132 C221
• Annotation score: 1

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

External links

• PDB: RCSB:5mko, PDBe:5mko, PDBj:5mko
• PDBsum: 5mko
• PubMed: 28655838
• UniProt: O58038|TTUA_PYRHO tRNA-5-methyluridine(54) 2-sulfurtransferase (Gene Name=ttuA)