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Structure of PDB 8y36 Chain Q Binding Site BS01

Receptor Information

>8y36 Chain Q (length=112) Species: 1280 (Staphylococcus aureus)

MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKV
LMSALANAEHNYDMNTDELVVKEAYANEGPTLKRFRPRAQGRASAINKRT
SHITIVVSDGKE

Ligand information

>8y36 Chain A (length=2885)

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

Structure summary

• PDB: 8y36 Synthetic macrolides overcoming MLS B K-resistant pathogens.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): V6 A7 R8 R11 R15 R18 R25 N40 K41 A42 K49 S53 A56 N57 H60 N61 N77 E78 P80 K83 R84 R86 P87 R88 A89 Q90 G91 R92 A93 A95 N97 K98 R99 H102
• Binding residue (residue number reindexed from 1): V6 A7 R8 R11 R15 R18 R25 N40 K41 A42 K49 S53 A56 N57 H60 N61 N77 E78 P80 K83 R84 R86 P87 R88 A89 Q90 G91 R92 A93 A95 N97 K98 R99 H102

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y36, PDBe:8y36, PDBj:8y36
• PDBsum: 8y36
• PubMed: 38992047
• UniProt: Q7A079|RL22_STAAW Large ribosomal subunit protein uL22 (Gene Name=rplV)

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