Structure of PDB 5xob Chain Z Binding Site BS01

Receptor Information

>5xob Chain Z (length=417) Species: 224325 (Archaeoglobus fulgidus DSM 4304)

MRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTIP
RGNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEELAV
KLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVGAEL
EDFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCNDVVV
CIPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDMHLI
GEEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEP
TKQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNPICP
SCGRRMESAGRGQGFRCKKCRTKADEKLREKVERELQPGFYEVPPSARRH
LSKPLIRMNVEGRHIFR

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5xob Chain Z Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xob Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
• Resolution: 2.48 Å
• Binding residue (original residue number in PDB): C352 C355 C373
• Binding residue (residue number reindexed from 1): C349 C352 C370
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.3.4.22: tRNA(Ile)(2)-agmatinylcytidine synthase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0016879 ligase activity, forming carbon-nitrogen bonds

Biological Process

• GO:0002101 tRNA wobble cytosine modification
• GO:0008033 tRNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5xob, PDBe:5xob, PDBj:5xob
• PDBsum: 5xob
• PubMed: 30121296
• UniProt: O28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)