Structure of PDB 8y39 Chain E Binding Site BS01

Receptor Information

>8y39 Chain E (length=206) Species: 1280 (Staphylococcus aureus)

ANYDVLKLDGTKSGSIELSDAVFGIEPNNSVLFEAINLQRASLRQGTHAV
KNRSAVSGGGRKPWKQKGTGRARQGTIRAPQWRGGGIVFGPTPRSYAYKM
PKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKK
VLVVTENEDVNVELSARNIPGVQVTTAQGLNVLDITNADSLVITEAAAKK
VEEVLG

Ligand information

>8y39 Chain A (length=2885)

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

Structure summary

• PDB: 8y39 Synthetic macrolides overcoming MLS B K-resistant pathogens.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): Q40 R41 S43 R45 Q46 T48 H49 A50 V51 N53 R54 S55 V57 S58 G59 R62 K63 K66 Q67 K68 G69 G71 R72 A73 R74 Q75 G76 R79 P81 Q82 R84 I88 F90 P92 R95 Y99 K100 P102 K103 K104 M105 R106 P134 K135 T136 K137 K151 L165 R168 N169 P171 N188
• Binding residue (residue number reindexed from 1): Q39 R40 S42 R44 Q45 T47 H48 A49 V50 N52 R53 S54 V56 S57 G58 R61 K62 K65 Q66 K67 G68 G70 R71 A72 R73 Q74 G75 R78 P80 Q81 R83 I87 F89 P91 R94 Y98 K99 P101 K102 K103 M104 R105 P133 K134 T135 K136 K150 L164 R167 N168 P170 N187

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y39, PDBe:8y39, PDBj:8y39
• PDBsum: 8y39
• PubMed: 38992047
• UniProt: P61060|RL4_STAAW Large ribosomal subunit protein uL4 (Gene Name=rplD)