Structure of PDB 2otj Chain D Binding Site BS02

Receptor Information

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

FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIR
EGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNL
VRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV

Ligand information

>2otj Chain 9 (length=122)

uuaggcggccacagcggugggguugccucccguacccaucccgaacacgg
aagauaagcccaccagcguuccggggaguacuggagugcgcgagccucug
ggaaacccgguucgccgccacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2otj The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): E12 M13 Q47 M48 P49 V50 V73 T74 R76 P137 G138 R140 V141 R144 D145 R149 P152 H155
• Binding residue (residue number reindexed from 1): E3 M4 Q33 M34 P35 V36 V59 T60 R62 P103 G104 R106 V107 R110 D111 R115 P118 H121
• Binding affinity: PDBbind-CN: Kd=2nM

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:2otj, PDBe:2otj, PDBj:2otj
• PDBsum: 2otj
• PubMed: 17321546
• UniProt: P14124|RL5_HALMA Large ribosomal subunit protein uL5 (Gene Name=rpl5)