Structure of PDB 8y39 Chain R Binding Site BS01

Receptor Information
>8y39 Chain R (length=89) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVA
SVNIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSIDLF
Ligand information
>8y39 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
cgaggggccgguuaccgaauucagacaaacuccgaaugccaauuaauuua
acuugggagucagaacaugggugauaagguccguguucgaaagggaaaca
gcccagaccaccagcuaaggucccaaaauauauguuaaguggaaaaggau
guggcguugcccagacaacuaggauguuggcuuagaagcagccaucauuu
aaagagugcguaauagcucacuagucgagugacacugcgccgaaaaugua
ccggggcuaaacauauuaccgaagcuguggauuguccuuuggacaauggu
aggagagcguucuaagggcguugaagcaugaucguaaggacauguggagc
gcuuagaagugagaaugccggugugaguagcgaaagacgggugagaaucc
cguccaccgauugacuaagguuuccagaggaaggcucguccgcucugggu
uagucggguccuaagcugaggccgacaggcguaggcgauggauaacaggu
ugauauuccuguaccaccuauaaucguuuuaaucgauggggggacgcagu
aggauaggcgaagcgugcgauuggauugcacgucuaagcaguaaggcuga
guauuaaauccgguacucguuaaggcugagcugugauggggagaagacau
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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PDB8y39 Synthetic macrolides overcoming MLS B K-resistant pathogens.
Resolution3.6 Å
Binding residue
(original residue number in PDB)
T13 E14 K15 K24 R32 N34 K35 T36 K39 M40 N54 I55 N57 Y58 K63 M65 Y68 G70 N73 K74 R76 I79
Binding residue
(residue number reindexed from 1)
T12 E13 K14 K23 R31 N33 K34 T35 K38 M39 N53 I54 N56 Y57 K62 M64 Y67 G69 N72 K73 R75 I78
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0000027 ribosomal large subunit assembly
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:8y39, PDBe:8y39, PDBj:8y39
PDBsum8y39
PubMed38992047
UniProtQ7A078|RL23_STAAW Large ribosomal subunit protein uL23 (Gene Name=rplW)

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