Structure of PDB 8ifc Chain d Binding Site BS03

Receptor Information

>8ifc Chain d (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

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: 8ifc Chain d Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ifc Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): T121 V122 R141
• Binding residue (residue number reindexed from 1): T121 V122 R141
• 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:8ifc, PDBe:8ifc, PDBj:8ifc
• PDBsum: 8ifc
• PubMed: 38227611
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)