Structure of PDB 8ekb Chain 2G Binding Site BS02

Receptor Information

>8ekb Chain 2G (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

Ligand information

>8ekb Chain 2B (length=120)

ucccccgugcccauagcggcguggaaccacccguucccauuccgaacacg
gaagugaaacgcgccagcgccgaugguacugggcgggcgaccgccuggga
gaguaggucggugcggggga

.<<<<<<<<<<....<<<<<<<<....<<<<<<...............>>
>..>>>...>>>>>>.>><<<.....<.<<<<<<<<....>>>>>>>>..
.>...>>>.>>>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ekb Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): P2 N27 V28 W29 E30 Q66 K67 A69 V70 V92 T93 R95 R96 R98
• Binding residue (residue number reindexed from 1): P1 N26 V27 W28 E29 Q65 K66 A68 V69 V91 T92 R94 R95 R97

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8ekb, PDBe:8ekb, PDBj:8ekb
• PDBsum: 8ekb
• PubMed: 36546783
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)