Structure of PDB 5ndg Chain d3 Binding Site BS02

Receptor Information

>5ndg Chain d3 (length=144) Species: 4932 (Saccharomyces cerevisiae)

GKGKPRGLNSARKLRVHRRNNRWAENNYKKRLLGTAFKSSPFGGSSHAKG
IVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE
VLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS

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: 5ndg Chain d3 Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): K62 A113
• Binding residue (residue number reindexed from 1): K61 A112
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P0CX29|RS23A_YEAST Small ribosomal subunit protein uS12A (Gene Name=RPS23A)