Structure of PDB 5dfe Chain YD Binding Site BS08

Receptor Information

>5dfe Chain YD (length=275) Species: 300852 (Thermus thermophilus HB8)

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARRKK

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: 5dfe Chain YD Residue 306

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dfe Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.
• Resolution: 3.09998 Å
• Binding residue (original residue number in PDB): Y62 R63 D85 N87 R88
• Binding residue (residue number reindexed from 1): Y61 R62 D84 N86 R87
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5dfe, PDBe:5dfe, PDBj:5dfe
• PDBsum: 5dfe
• PubMed: 27681416
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)