Structure of PDB 8cee Chain M Binding Site BS01

Receptor Information
>8cee Chain M (length=108) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEE
LGKIRDIIDKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNS
KNNARTRK
Ligand information
>8cee Chain A (length=1333) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
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PDB8cee Structural basis of ribosomal 30S subunit degradation by RNase R
Resolution3.7 Å
Binding residue
(original residue number in PDB)		K13 R14 I17 F23 G24 I25 G26 R27 T28 T29 R44 N76 Y86 R87 R90 H91 L95 P96 V97 R98 Q100 N101 S102 K103 N104 N105 A106 R107 T108 R109 K110
Binding residue
(residue number reindexed from 1)		K11 R12 I15 F21 G22 I23 G24 R25 T26 T27 R42 N74 Y84 R85 R88 H89 L93 P94 V95 R96 Q98 N99 S100 K101 N102 N103 A104 R105 T106 R107 K108
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:8cee, PDBe:8cee, PDBj:8cee
PDBsum8cee
PubMed38326618
UniProtP20282|RS13_BACSU Small ribosomal subunit protein uS13 (Gene Name=rpsM)

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