Structure of PDB 2qex Chain D Binding Site BS02

Receptor Information

>2qex Chain D (length=140) Species: 2238 (Haloarcula marismortui)

FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIR
EGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNL
VRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV

Ligand information

>2qex Chain 9 (length=122)

uuaggcggccacagcggugggguugccucccguacccaucccgaacacgg
aagauaagcccaccagcguuccggggaguacuggagugcgcgagccucug
ggaaacccgguucgccgccacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2qex Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): M13 R14 Q47 M48 P49 V50 V73 T74 R76 P137 R140 V141 K143 R144 D145 R149 P152 K154 H155
• Binding residue (residue number reindexed from 1): M4 R5 Q33 M34 P35 V36 V59 T60 R62 P103 R106 V107 K109 R110 D111 R115 P118 K120 H121

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:2qex, PDBe:2qex, PDBj:2qex
• PDBsum: 2qex
• PubMed: 17664317
• UniProt: P14124|RL5_HALMA Large ribosomal subunit protein uL5 (Gene Name=rpl5)