Structure of PDB 5ndk Chain D5 Binding Site BS02

Receptor Information
>5ndk Chain D5 (length=135) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEYRLKAYYREGEKPSALRRAGKLPGVMYNRHLNRKVYVDLVEFDKVFRQ
ASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYV
PLRFRDILVKVSPRNIPEFIEVLPPGVELAVSPEE
Ligand information
>5ndk Chain 1J (length=122) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aaucccccgugcccauagcggcguggaaccacccguucccauuccgaaca
cggaagugaaacgcgccagcgccgaugguacugggcgggcgaccgccugg
gagaguaggucggugcggggga
..<<<<<<<<<<<....<<<<<<<<....<<<<<<...............
>>>..>>>...>>>>>>.>><<<.......<<<<<<<<....>>>>>>>>
.......>>>.>>>>>>>>>>>
Receptor-Ligand Complex Structure
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PDB5ndk Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		R10 Y29 N34 R72 Q73 N75 R79 E84 H85 D87 F89
Binding residue
(residue number reindexed from 1)		R10 Y29 N34 R72 Q73 N75 R79 E84 H85 D87 F89
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Cellular Component
External links
PDB RCSB:5ndk, PDBe:5ndk, PDBj:5ndk
PDBsum5ndk
PubMed29208708
UniProtQ5SHZ1|RL25_THET8 Large ribosomal subunit protein bL25 (Gene Name=rplY)

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