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Structure of PDB 8y37 Chain O Binding Site BS01

Receptor Information

>8y37 Chain O (length=116) Species: 1280 (Staphylococcus aureus)

PRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRR
QRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAIS
DEKAFAQLVTKAKDAL

Ligand information

>8y37 Chain A (length=2884)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaaugggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuagaguuacaaaggacgacauuagacgaaucaucuggaaaga
ugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuuga
guggauccugaguacgacggagcacgugaaauuccgucggaaucugggag
gaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagua
ccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaaccu
gaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgug
ccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagcag
uaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauuu
ggucguagacccgaaaccaggugaucuacccuuggucagguugaagaaug
gaggaccgaaccgacuuacguugaaaagugagcggaugaacugaggguag
cggagaaauuccaaucgaaccuggagauagcugguucucuccgaaauagc
uuuagggcuagccucaagugaugauuauuggagguagagcacuguuugga
cgaggggccgguuaccgaauucagacaaacuccgaaugccaauuaauuua
acuugggagucagaacaugggugauaagguccguguucgaaagggaaaca
gcccagaccaccagcuaaggucccaaaauauauguuaaguggaaaaggau
guggcguugcccagacaacuaggauguuggcuuagaagcagccaucauuu
aaagagugcguaauagcucacuagucgagugacacugcgccgaaaaugua
ccggggcuaaacauauuaccgaagcuguggauuguccuuuggacaauggu
aggagagcguucuaagggcguugaagcaugaucguaaggacauguggagc
gcuuagaagugagaaugccggugugaguagcgaaagacgggugagaaucc
cguccaccgauugacuaagguuuccagaggaaggcucguccgcucugggu
uagucggguccuaagcugaggccgacaggcguaggcgauggauaacaggu
ugauauuccuguaccaccuauaaucguuuuaaucgauggggggacgcagu
aggauaggcgaagcgugcgauuggauucacgucuaagcaguaaggcugag
uauuaaauccgguacucguuaaggcugagcugugauggggagaagacauu
gugucuucgagucguugauuucacacugccgagaaaagccucuagauaga
aaauaggugcccguaccgcaaaccgacacagguagucaagaugagaauuc
uaaggugagcgagcgaacucucguuaaggaacucggcaaaaugaccccgu
aacuucgggagaaggggugcucuuuaggguuaacgcccagaagagccgca
gugaauaggcccaagcgacuguuuaucaaaaacacaggucucugcuaaac
cguaaggugauguauaggggcugacgccugcccggugcuggaagguuaag
aggagugguuagcuucugcgaagcuacgaaucgaagccccaguaaacggc
ggccguauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
acccgcacgaaaggcguaacgauuugggcacugucucaacgagagacucg
gugaaaucauaguaccugugaagaugcagguuacccgcgacaggacggaa
agaccccguggagcuuuacuguagccugauauugaaauucggcacagcuu
guacaggauagguaggagccuuugaaacgugagcgcuagcuuacguggag
gcgcuggugggauacuacccuagcuguguuggcuuucuaacccgcaccac
uuaucguggugggagacagugucaggcgggcaguuugacuggggcggucg
ccuccuaaaagguaacggaggcgcucaaagguucccucagaaugguugga
aaucauucauagaguguaaaggcauaagggagcuugacugcgagaccuac
aagucgagcagggucgaaagacggacuuagugauccggugguuccgcaug
gaagggccaucgcucaacggauaaaagcuaccccggggauaacaggcuua
ucucccccaagaguucacaucgacggggagguuuggcaccucgaugucgg
cucaucgcauccuggggcuguagucggucccaaggguugggcuguucgcc
cauuaaagcgguacgcgagcuggguucagaacgucgugagacaguucggu
cccuauccgucgugggcguaggaaauuugagaggagcuguccuuaguacg
agaggaccgggauggacauaccucugguguaccaguugucgugccaacgg
cauagcuggguagcuauguguggacgggauaagugcugaaagcaucuaag
caugaagccccccucaagaugagauuucccaacuucgguuauaagauccc
ucaaagaugaugagguuaauagguucgagguggaagcauggugacaugug
gagcugacgaauacuaaucgaucgaagacuuaau

<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<...<<<))..)).>>>.....
.>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<......<<....
>>.......>>>>.>...................<<<<<......<<...
..>>.....>>>>>..(((....<<..<<<<....>>>>..>>......<
<<<<<<<...<<<.......<<<<<<<<<<.<<<...<<<<<......>>
>>>((......<<<.....))>>>...>>>...>>>>>>>>>>>>>...>
>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<
..<<<<>>>>>..)))......]].>>>>>>>.]]...............
<<....>>....]].........<<<<....>>>>...............
...>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...
<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<<.
....>>>...>>>...<<....>>..<<<<.....>>>>.....>>>>>.
>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<.........
....>>>...<<<.<<<<<........>>>>>>>>....>>>>>>>>>..
.<<<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<
<....>>>>><<<<<<<<<...<<<<<<<<<.....<<<...<<<<<<<<
....<.........>....>>>>>>>>..>>.>.....>>>>.>>>>>..
>>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>....<<<.....
.>>>...<<<<.<<<...<<<(((.....<<<<<<...........<<..
<<<<.<<<<...........<..<<.....................>>..
.....................>.......>>>>.>>>>.>>.........
..))).....>>>>>>.>>>...>>>>>>><<<<<<<...>>>>>>>...
.>>>>>>..<<<<<<<.<<......<<<<<.<<....>>.>>>>>...>>
.>>>>>>>........>>>>>><......<<....<<<<<<.......>>
>>>><<<<....<<<<<.<<<..<<<<<<...<<.....>>.>>>>>>..
..((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<<<<.
.......>>>>>))<<<<<<<............<...<<<<....<<<<.
.<<...<<<<<.<.<.......{....>.>.............<<<....
.<<<......>>>..........>>>........................
...........>>>>>....>>...>>>>.........>>>>..>.....
..>>>>>>>>>>>.>>>.....<<......>>>>>>>.<<<<....>.>>
>..>>>>..<<<<....<<<<<<<<.<<...............<<<<<..
.............>>>>><<<<<<<.<<<<....>>>>.>>>>>>>....
........<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<
<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<
<...<<<<<..<<....>>...>>>>>...>>...>>>>>>>>..>>>>>
<<<<<.....>>>>>........<...........<<<<<<.....>>>>
>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>
>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[..
....<<<<.[[<<<<..<<<<..<<<<<<<<<.<<<<.<<<.....<<..
...........<.<<..<<.........<.<<<......>>>.>......
>>............>>.>....>>.....>>>.>>>>....<<.<<<<<<
.....>>>>>>>>.....>>>>>>>>>...>>>>..<<<<.....>>>><
<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.....
..>>>>>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<....
..>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>>
>..))>>>>>>>.............>>>>..]]>>>>.......<<<<.<
.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<<
<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>
>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>...
.]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.......
........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<.}..>>>>
>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>
>>>....>>>.>>>>.......>>>>>>>.<<......>>....<<<<<<
<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>.
..>>>..>>>>>.>>>...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y37 Synthetic macrolides overcoming MLS B K-resistant pathogens.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): P2 R3 V4 K5 T10 R11 R13 R14 K15 K16 K19 K22 G23 Y24 F25 G26 S27 K28 H29 Y32 K33 V34 K36 Q37 Q38 K41 S42 Y45 A46 F47 R48 D49 R50 R51 Q52 R53 K54 R55 F57 R58 K59 W61 I62 N66 R70 S75 Y76 S77 R78 N81 N91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 V3 K4 T9 R10 R12 R13 K14 K15 K18 K21 G22 Y23 F24 G25 S26 K27 H28 Y31 K32 V33 K35 Q36 Q37 K40 S41 Y44 A45 F46 R47 D48 R49 R50 Q51 R52 K53 R54 F56 R57 K58 W60 I61 N65 R69 S74 Y75 S76 R77 N80 N90 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly

Cellular Component

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

External links

• PDB: RCSB:8y37, PDBe:8y37, PDBj:8y37
• PDBsum: 8y37
• PubMed: 38992047
• UniProt: P66109|RL20_STAAW Large ribosomal subunit protein bL20 (Gene Name=rplT)

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