Structure of PDB 8byv Chain l Binding Site BS01

Receptor Information
>8byv Chain l (length=135) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTINQLVRKPRQSKIKKSDSPALNKGFNSKKKKFTDLNSPQKRGVCTRVG
TMTPKKPNSALRKYARVRLSNNIEINAYIPGIGHNLQEHSVVLVRGGRVK
DLPGVRYHIVRGALDTSGVDGRRQGRSLYGTKKPK
Ligand information
>8byv Chain a (length=1533) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggagaguuugauccuggcucaggaugaacgcuggcggcgugccuaauaca
ugcaagucgagcgaacggacgagaagcuugcuucucugauguuagcggcg
gacgggugaguaacacguggauaaccuaccuauaagacugggauaacuuc
gggaaaccguagcuaauaccggauaauauuuugaaccgcaugguucaaaa
gugaaagacggucuugcugucacuuauagauggauccgcgcugcauuagc
uaguugguaagguaacggcuuaccaaggcaacgaugcauagccgaccuga
gagggugaucggccacacuggaacugagacacgguccagacuccuacggg
aggcagcaguagggaaucuuccgcaaugggcgaaagccugacggagcaac
gccgcgugagugaugaaggucuucggaucguaaaacucuguuauuaggga
agaacauauguguaaguaacugugcacaucuugacgguaccuaaucagaa
agccacggcuaacuacgugccagcagccgcgguaauacguagguggcaag
cguuauccggaauuauugggcguaaagcgcgcguaggcgguuuuuuaagu
cugaugugaaagcccacggcucaaccguggagggucauuggaaacuggaa
aacuugagugcagaagaggaaaguggaauuccauguguagcggugaaaug
cgcagagauauggaggaacaccaguggcgaaggcgacuuucuggucugua
acugacgcugaugugcgaaagcguggggaucaaacaggauuagauacccu
gguaguccacgccguaaacgaugagugcuaaguguuaggggguuucccgc
cccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacgac
cgcaagguugaaacucaaaggaauugacggggacccgcacaagcggugga
gcaugugguuuaauucgaagcaacgcgaagaaccuuaccaaaucuugaca
uccuuugacaacucuagagauagagccuuccccuucgggggacaaaguga
cagguggugcaugguugucgucagcucgugucgugagauguuggguuaag
ucccgcaacgagcgcaacccuuaagcuuaguugccaucauuaaguugggc
acucuaaguugacugccggugacaaaccggaggaagguggggaugacguc
aaaucaucaugccccuuaugauuugggcuacacacgugcuacaauggaca
auacaaagggcagcgaaaccgcgaggucaagcaaaucccauaaaguuguu
cucaguucggauuguagucugcaacucgacuacaugaagcuggaaucgcu
aguaaucguagaucagcaugcuacggugaauacguucccgggucuuguac
acacccgucacaccacgagaguuuguaacacccgaagccgguggaguaac
cuuuuaggagcuagccgucgaaggugggacaaaugauuggggugaagucg
gguagccguaucggaaggugcggcuggaucacc
...<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<.
<<<..<<<..<<.<<<<....<<<........>>>....>>>>.>>>>>.
.....<<........<<<<<<<..<<...<<<<<<<.<<<<.....<<.<
<<....>>>.>>......>>>>......<<<<<<<<<....>>>>>>>>>
......<<<<<<...>>>>>>.>>>>>>>..>>>>>>>>>.<<<....<<
<..<<<<<<<<.......>>>>>>>>>>>......>>>..<<<<<<<<..
..>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>
>>...>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>
>>>>>..<<<<......<<<<....>>>>.....>>>>...<<<<<<<..
..........<<............>>.............>>>>>>...>.
.<<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>
>>>>>>>>..........<<<((.....<<<<<..<<<.<<<<<<<.<<<
<<<<<<.......<<<<<<.....>>>>>>.....>>>>>>>..>>>>>>
>>>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>
>......>>>>>>>>...........<<....>>.>>>>>>>..>>>>>.
>>>...>>>..>>>>>....<<<<<<<...<...<<<<.<.....>.>>>
>...>>>>>>>>..........<<<<<<..<<<<<<<<<<<<<.....>>
>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<......<<<
<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<..<<<<<..<
<<<<<<<........<<........>>..........<<<<<<<......
<<<<<......<<<<<....>>>>>.....<<<....>>>....>>>.>>
.<<<.<<<...<<<<<<......<<<<<<<<<....>>>..<<<<.....
.>>>>..>>>>>>.....<<<<.<<<<<<...<<<..<<......>>>>>
....>>>>>>.....<<<<<.....>>>>>........>>>>.......>
.>>>...>>.>>>>>>...>>>>>>>......>>>>>>>>.....<<<<<
<<.....<<<..<<...<<<....>>>...>>....>>>.....>>>>>>
>......<....<<<<<<<........>>>>>>>....>.....>>>>>.
....<<<<<<<.........>>>>>>>......>....>>>>>>>>>>.>
>....<<...<<<<.<<<...<<<<<..<<<<....<.<<<<..<<<..<
<<...>>>.>>>.>>>>.>...>>>>..>>>>>...>>>.>>>>....>>
...<<<<<<<<<....>>>>>>>>>........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8byv Structural characteristic of RbfA from S. aureus
Resolution2.89 Å
Binding residue
(original residue number in PDB)		P2 T3 N5 L7 R9 R12 Q13 K15 K18 S19 N25 N29 N39 S40 P41 Q42 R44 K57 N59 S60 A61 R63 K64 S71 Y79 P81 G82 I83 R96 G97 K101 P104 A114 R123 R124 Q125 G126 R127 S128 L129 G131 T132 K133 K134
Binding residue
(residue number reindexed from 1)		P1 T2 N4 L6 R8 R11 Q12 K14 K17 S18 N24 N28 N38 S39 P40 Q41 R43 K56 N58 S59 A60 R62 K63 S70 Y78 P80 G81 I82 R95 G96 K100 P103 A113 R122 R123 Q124 G125 R126 S127 L128 G130 T131 K132 K133
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8byv, PDBe:8byv, PDBj:8byv
PDBsum8byv
PubMed36768442
UniProtP0A0H0|RS12_STAA8 Small ribosomal subunit protein uS12 (Gene Name=rpsL)

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