Structure of PDB 8cdu Chain J Binding Site BS01

Receptor Information

>8cdu Chain J (length=108) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

QYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTL
TETAGTYDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLL
TRDARMKE

Ligand information

>8cdu Chain A (length=1333)

ggagaguuugauccuggcucaggacgaacgcuggcggcgugccuaauaca
ugcaagucgagcggacagauguuagcggcggacgggugaguaacacgugg
guaaccugccuguaagacugggauaacuccgggaaaccggggcuaauacc
ggaugguuguuugaaccgcaugguucaaacauaaaagguggcuucggcua
ccacuuacagauggacccgcggcgcauuagcuaguuggugagguaacggc
ucaccaaggcgacgaugcguagccgaccugagagggugaucggccacacu
gggacugagacacggcccagacuccuacgggaggcagcaguagggaaucu
uccgcaauggacgaaagucugacggagcaacgccgcgugagugaugaagg
uuuucggaucguaaagcucuguuguuagggaagaacaagugccguucgaa
uagggcgguaccuugacgguaccuaaccagaaagccacggcuaacuacgu
gccagcagccgcgguaauacguagguggcaagcguuguccggaauuauug
ggcguaaagggcucgcaggcgguuucuuaagucugaugugaaagcccccg
gcucaaccggggagggucauuggaaacuggggaacuugagugcagaagag
gagaguggaauuccacguguagcggugaaaugcguagagauguggaggaa
caccaguggcgaaggcgacucucuggucuguaacugacgcugaggagcga
aagcgcgccguaaacgaugagugcuaaguguuaggggguuuccgccccuu
agugcugcagcuaacgcauuaagcacuccgccuggggaguacggucgcaa
gacugaaacucaaaggaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaaacgcgaagaaccuuaccaggucuugacauccucuga
caauccuagagauaggacguccccuucgggggcagagugacagguggugc
augguugucgucagcucgugucgugagauguuggguuaagucccgcaacg
agcgcaacccuugaucuuaguugccagcauucaguugggcacucuaaggu
gacugccggugacaaaccggaggaagguggggaugacgucaaaucaucau
gccccuuaugaccugggcuacacacgugcuacaauggacagaacaaaggg
cagcgaaaccgcgagguuaagccaaucccacaaaucuguucucaguucgg
aucgcagucugcaacucgacugcgugaagcuggaaucgcuaguaaucgcg
gaucagcaugccgcggugaauacguucccgggc

...<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<.
<<<..<<<..<<.<<<<..>>>>.>>>>>......<<........<<<<<
<<..<<...<<<<<<<.<<<<.....<<<<<<....>>>>>>......>>
>>.....<<<<<<<<<<....>>>>>>>>>>.....<<<<<<<..>>>>>
>>.>>>>>>>..>>>>>>>>>.<<<....<<<..<<<<<<<<.......>
>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<
<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>........
.<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<
<<....>>>>.....>>>>...<<<<<<<.......<.<<<<<<<<<...
..>>>>>>>>>.>........>>>>>>...>..<<<<<(((...<<<<<.
....<<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........
<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<.......<<<<<
<.....>>>>>>.....>>>>>>>..>>>>>>>>>...<<<<<<<<...<
<<<<<<.......<<<<......<......>.........>>>>......
........<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>..
..<<..>>..........<<<<<<..<<<<<<<<<<<<<....>>>>>>>
>>>>>>...<<..))>>.....>>>>>>.>>>.<<<......<<<<....
>>>>....>>>..)))).].........<<<<.<<.<<<<<<..<<<<<<
<<<<.........................<<<<<<<.......<<<<...
....<<<<....>>>>.....<<<....>>>...>>>.>..<<<.<<<..
<<<<<<.<.....<<<<<<<<<....>>>..<<<<......>>>>..>>>
>>>.....<<<<.<<<<<<....<..............>.....>>>>>>
.....<<<<<.....>>>>>........>>>>.....>...>>>...>>>
>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<
..<<..<<<<....>>>>..>>....>>>.....>>>>>>>......<..
..<<<<<<<........>>>>>>>....>.....>>>>>>....<<<<<<
<.........>>>>>>>......>>...>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cdu Structural basis of ribosomal 30S subunit degradation by RNase R
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): Y7 T9 R11 R12 K13 S14 R18 R20 G69 G70 G71 S73 Q75 R85 R95 K99 R100 L104 R106 A108 R109 M110 K111 E112
• Binding residue (residue number reindexed from 1): Y3 T5 R7 R8 K9 S10 R14 R16 G65 G66 G67 S69 Q71 R81 R91 K95 R96 L100 R102 A104 R105 M106 K107 E108

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cdu, PDBe:8cdu, PDBj:8cdu
• PDBsum: 8cdu
• PubMed: 38326618
• UniProt: P21470|RS9_BACSU Small ribosomal subunit protein uS9 (Gene Name=rpsI)