Structure of PDB 5wdt Chain z Binding Site BS06

Receptor Information

>5wdt Chain z (length=393) Species: 562 (Escherichia coli)

SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQID
NAPEEKARGITINTSHVEYDTPTRHYAHVDCPGAADYVKNMITGAAQMDG
AILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVE
MEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIP
EPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKET
QKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMV
MPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5wdt Chain z Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wdt Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): T25 T61
• Binding residue (residue number reindexed from 1): T25 T61
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0097216 guanosine tetraphosphate binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane
• GO:0032045 guanyl-nucleotide exchange factor complex

External links

• PDB: RCSB:5wdt, PDBe:5wdt, PDBj:5wdt
• PDBsum: 5wdt
• PubMed: 29733411
• UniProt: P0CE48|EFTU2_ECOLI Elongation factor Tu 2 (Gene Name=tufB)