Structure of PDB 8y38 Chain U Binding Site BS01

Receptor Information
>8y38 Chain U (length=82) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGR
GGDDTLFAKIDGVVKFERKGRDKKQVSVYAVA
Ligand information
>8y38 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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PDB8y38 Synthetic macrolides overcoming MLS B K-resistant pathogens.
Resolution2.58 Å
Binding residue
(original residue number in PDB)
K12 G14 V15 S16 S17 T18 N20 R22 D23 S24 E25 S26 K27 R28 K32 R33 A34 D35 G36 Q37 T40 G41 G42 S43 I44 Y46 R47 R49 G50 T51 Y54 G62 G63 D64 D65 T66 F68 K70 K84 K85
Binding residue
(residue number reindexed from 1)
K1 G3 V4 S5 S6 T7 N9 R11 D12 S13 E14 S15 K16 R17 K21 R22 A23 D24 G25 Q26 T29 G30 G31 S32 I33 Y35 R36 R38 G39 T40 Y43 G51 G52 D53 D54 T55 F57 K59 K73 K74
External links
PDB RCSB:8y38, PDBe:8y38, PDBj:8y38
PDBsum8y38
PubMed38992047
UniProtP66134|RL27_STAAW Large ribosomal subunit protein bL27 (Gene Name=rpmA)

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