Structure of PDB 8y37 Chain N Binding Site BS01

Receptor Information
>8y37 Chain N (length=114) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIK
RRGGGVSETFTVRKISSGVGVERTFPLHTPKIEKIEVKRRGKVRRAKLYY
LRSLRGKAARIQEI
Ligand information
>8y37 Chain A (length=2884) [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
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
Global viewLocal viewStructure summary

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PDB8y37 Synthetic macrolides overcoming MLS B K-resistant pathogens.
Resolution2.53 Å
Binding residue
(original residue number in PDB)
H4 R23 K51 R53 G54 G55 T60 R95 R96 A97 K98 Y100
Binding residue
(residue number reindexed from 1)
H3 R22 K50 R52 G53 G54 T59 R94 R95 A96 K97 Y99
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8y37, PDBe:8y37, PDBj:8y37
PDBsum8y37
PubMed38992047
UniProtQ8NX05|RL19_STAAW Large ribosomal subunit protein bL19 (Gene Name=rplS)

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