Structure of PDB 6xqd Chain 2D Binding Site BS04

Receptor Information

>6xqd Chain 2D (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: 6xqd Chain 2A Residue 3443

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xqd Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G57 H58 R60 W214 L215
• Binding residue (residue number reindexed from 1): G56 H57 R59 W213 L214
• 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:6xqd, PDBe:6xqd, PDBj:6xqd
• PDBsum: 6xqd
• PubMed: 32817463
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)