Structure of PDB 5mdy Chain V Binding Site BS02

Receptor Information

>5mdy Chain V (length=94) Species: 83333 (Escherichia coli K-12)

MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNM
QAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Ligand information

>5mdy Chain 3 (length=120)

ugccuggcggccguagcgcgguggucccaccugaccccaugccgaacuca
gaagugaaacgccguagcgccgaugguaguguggggucuccccaugcgag
aguagggaacugccaggcau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mdy Translational termination without a stop codon.
• Resolution: 3.35 Å
• Binding residue (original residue number in PDB): R9 G13 K14 S17 R18 R19 R21 I29 Y31 Q75 Q78 H88 D90
• Binding residue (residue number reindexed from 1): R9 G13 K14 S17 R18 R19 R21 I29 Y31 Q75 Q78 H88 D90

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:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0009314 response to radiation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mdy, PDBe:5mdy, PDBj:5mdy
• PDBsum: 5mdy
• PubMed: 27934701
• UniProt: P68919|RL25_ECOLI Large ribosomal subunit protein bL25 (Gene Name=rplY)