Structure of PDB 5wf0 Chain D Binding Site BS02

Receptor Information

>5wf0 Chain D (length=208) Species: 562 (Escherichia coli)

IGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVT
TGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELF
ADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQT
PGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDL
IVKPAVKA

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: 5wf0 Chain D Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wf0 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: 3.6 Å
• Binding residue (original residue number in PDB): K123 N126
• Binding residue (residue number reindexed from 1): K122 N125
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5wf0, PDBe:5wf0, PDBj:5wf0
• PDBsum: 5wf0
• PubMed: 29733411
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)