Structure of PDB 8y36 Chain W Binding Site BS01

Receptor Information
>8y36 Chain W (length=67) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIA
RLKTVAREREIEQSKAN
Ligand information
>8y36 Chain A (length=2885) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaaugggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuagaguuacaaaggacgacauuagacgaaucaucuggaaaga
ugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuuga
guggauccugaguacgacggagcacgugaaauuccgucggaaucugggag
gaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagua
ccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaaccu
gaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgug
ccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagcag
uaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauuu
ggucguagacccgaaaccaggugaucuacccuuggucagguugaagaaug
gaggaccgaaccgacuuacguugaaaagugagcggaugaacugaggguag
cggagaaauuccaaucgaaccuggagauagcugguucucuccgaaauagc
uuuagggcuagccucaagugaugauuauuggagguagagcacuguuugga
cgagggggguuaccgaauucagacaaacuccgaaugccaauuaauuuaac
uugggagucagaacaugggugauaagguccguguucgaaagggaaacagc
ccagaccaccagcuaaggucccaaaauauauguuaaguggaaaaggaugu
ggcguugcccagacaacuaggauguuggcuuagaagcagccaucauuuaa
agagugcguaauagcucacuagucgagugacacugcgccgaaaauguacc
ggggcuaaacauauuaccgaagcuguggauuguccuuuggacaaugguag
gagagcguucuaagggcguugaagcaugaucguaaggacauguggagcgc
uuagaagugagaaugccggugugaguagcgaaagacgggugagaaucccg
uccaccgauugacuaagguuuccagaggaaggcucguccgcucuggguua
gucggguccuaagcugaggccgacaggcguaggcgauggauaacagguug
auauuccuguaccaccuauaaucguuuuaaucgauggggggacgcaguag
gauaggcgaagcgugcgauuggauugcacgucuaagcaguaaggcugagu
auuagaaauccgguacucguuaaggcugagcugugauggggagaagacau
ugugucuucgagucguugauuucacacugccgagaaaagccucuagauag
aaaauaggugcccguaccgcaaaccgacacagguagucaagaugagaauu
cuaaggugagcgagcgaacucucguuaaggaacucggcaaaaugaccccg
uaacuucgggagaaggggugcucuuuaggguuaacgcccagaagagccgc
agugaauaggcccaagcgacuguuuaucaaaaacacaggucucugcuaaa
ccguaaggugauguauaggggcugacgccugcccggugcuggaagguuaa
gaggagugguuagcuucugcgaagcuacgaaucgaagccccaguaaacgg
cggccguauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gacccgcacgaaaggcguaacgauuugggcacugucucaacgagagacuc
ggugaaaucauaguaccugugaagaugcagguuacccgcgacaggacgga
aagaccccguggagcuuuacuguagccugauauugaaauucggcacagcu
uguacaggauagguaggagccuuugaaacgugagcgcuagcuuacgugga
ggcgcuggugggauacuacccuagcuguguuggcuuucuaacccgcacca
cuuaucguggugggagacagugucaggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcucaaagguucccucagaaugguugg
aaaucauucauagaguguaaaggcauaagggagcuugacugcgagaccua
caagucgagcagggucgaaagacggacuuagugauccggugguuccgcau
ggaagggccaucgcucaacggauaaaagcuaccccggggauaacaggcuu
aucucccccaagaguucacaucgacggggagguuuggcaccucgaugucg
gcucaucgcauccuggggcuguagucggucccaaggguugggcuguucgc
ccauuaaagcgguacgcgagcuggguucagaacgucgugagacaguucgg
ucccuauccgucgugggcguaggaaauuugagaggagcuguccuuaguac
gagaggaccgggauggacauaccucugguguaccaguugucgugccaacg
gcauagcuggguagcuauguguggacgggauaagugcugaaagcaucuaa
gcaugaagccccccucaagaugagauuucccaacuucgguuauaagaucc
cucaaagaugaugagguuaauagguucgagguggaagcauggugacaugu
ggagcugacgaauacuaaucgaucgaagacuuaau
<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<......<<....
>>.......>>>>.>...................<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<<..>>>>>>>>>......<
<<<<<<<...<<<.......<<<<<<<<<<.<<<...<<<<<......>>
>>>((......<<<.....))>>>...>>>...>>>>>>>>>>>>>...>
>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<
..<<<<>>>>>..)))......]].>>>>>>>.]]...............
<<....>>....]].........<<<<....>>>>...............
...>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...
<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<<.
....>>>...>>>...<<....>>..<<<<.....>>>>.....>>>>>.
>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<<........
..>.>>>...<<<.<<<<<........>>>>>>>>....>>>>>>>>>..
.<<<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<
<....>>>>><<<<<<<<<...<<<<<<<<<.....<<<...<<<<<<<<
...<<.......>>...>>>>>>>>..>>.>.....>>>>.>>>>>..>>
>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>....<<<......>
>>...<<<<.<<<...<<<(((.....<<<<<<...........<<..<<
<<.<<<<...........<..<<.....................>>....
...................>.......>>>>.>>>>.>>...........
))).....>>>>>>.>>>...>>>>>>><<<<<<<...>>>>>>>....>
>>>>>..<<<<<<<.<<......<<<<<.<<....>>.>>>>>...>>.>
>>>>>>........>>>>>><......<<....<<<<<<.......>>>>
>><<<<....<<<<<.<<<..<<<<<<...<<.....>>.>>>>>>....
((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<<<<...
.....>>>>>))<<<<<<<............<...<<<<....<<<<..<
<<..<<<<<.<.......{.{.......>.............<<<....<
<<..........>>>.........>>>.......................
............>>>>>...>>>...>>>>.........>>>>..>....
...>>>>>>>>>>>.>>>.....<<......>>>>>>>.<<<<....>.>
>>..>>>>..<<<<....<<<<<<<<.<<...............<<<<<.
...<....>.....>>>>><<<<<<<.<<<<....>>>>.>>>>>>>...
.........<<<<<<<<<..<<<.........>>>..<<<<<<<.....<
<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...
<<...<<<<<..<<....>>...>>>>>...>>...>>>>>>>>..>>>>
><<<<<.....>>>>>........<...........<<<<<<.....>>>
>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>
>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[.
.....<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<<.<<<........
............<<<<..<<.........<.<<<<....>>>>.>.....
.>>............>>>>...........>>>.>>>>....<<.<<<<<
<.....>>>>>>>>.....>>>>>>>>>..>>>>>..<<<<.....>>>>
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<...
...>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>
>>..))>>>>>>>.............>>>>..]]>>>>.......<<<<.
<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<
<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>
>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>..
..]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<......
.........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<.}.}>>>
>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>
>>>>....>>>.>>>>.......>>>>>>>.<<......>>....<<<<<
<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>
...>>>..>>>>>.>>>...>>>>....>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8y36 Synthetic macrolides overcoming MLS B K-resistant pathogens.
Resolution2.65 Å
Binding residue
(original residue number in PDB)
R7 E39 T40 A41 I43 R44 R47 K48 R52 K54 T55 R58 E59
Binding residue
(residue number reindexed from 1)
R6 E38 T39 A40 I42 R43 R46 K47 R51 K53 T54 R57 E58
Gene Ontology
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8y36, PDBe:8y36, PDBj:8y36
PDBsum8y36
PubMed38992047
UniProtP66174|RL29_STAAW Large ribosomal subunit protein uL29 (Gene Name=rpmC)

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