Structure of PDB 1yij Chain D Binding Site BS02

Receptor Information

>1yij Chain D (length=140) Species: 2238 (Haloarcula marismortui)

FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIR
EGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNL
VRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV

Ligand information

>1yij Chain 9 (length=122)

uuaggcggccacagcggugggguugccucccguacccaucccgaacacgg
aagauaagcccaccagcguuccagggaguacuggagugcgcgagccucug
ggaaauccgguucgccgccacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yij Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): E12 M13 R14 R17 M48 P49 V50 V73 T74 R76 P137 G138 R140 R144 D145 R149 P152 K154 H155
• Binding residue (residue number reindexed from 1): E3 M4 R5 R8 M34 P35 V36 V59 T60 R62 P103 G104 R106 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:1yij, PDBe:1yij, PDBj:1yij
• PDBsum: 1yij
• PubMed: 15851032
• UniProt: P14124|RL5_HALMA Large ribosomal subunit protein uL5 (Gene Name=rpl5)