Structure of PDB 6s0x Chain D Binding Site BS01

Receptor Information

>6s0x Chain D (length=215) Species: 1280 (Staphylococcus aureus)

TKGILGRKIGMTQVFGENGELIPVTVVEAKENVVLQKKTVEVDGYNAIQV
GFEDKKAYKKDAKSNKYANKPAEGHAKKADAAPKRFIREFRNVDVDAYEV
GQEVSVDTFVAGDVIDVTGVSKGKGFQGAIKRHGQSRGPMSHGSHFHRAP
GSVGMASDASRVFKGQKMPGRMGGNTVTVQNLEVVQVDTENKVILVKGNV
PGPKKGLVEIRTSIK

Ligand information

>6s0x Chain A (length=2905)

uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaaugggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuacggaguuacaaaggacgacauuagacgaaucaucuggaaa
gaugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuu
gaguggauccugaguacgacggagcacgugaaauuccgucggaaucuggg
aggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccag
uaccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaac
cugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcg
ugccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagc
aguaaauguggagccguagcgaaagcgagucugaauagggcguuuaguau
uuggucguagacccgaaaccaggugaucuacccuuggucagguugaaguu
cagguaacacugaauggaggaccgaaccgacuuacguugaaaagugagcg
gaugaacugaggguagcggagaaauuccaaucgaaccuggagauagcugg
uucucuccgaaauagcuuuagggcuagccucaagugaugauuauuggagg
uagagcacuguuuggacgaggggccgguuaccgaauucagacaaacuccg
aaugccaauuaauuuaacuugggagucagaacaugggugauaagguccgu
guucgaaagggaaacagcccagaccaccagcuaaggucccaaaauauaug
uuaaguggaaaaggauguggcguugcccagacaacuaggauguuggcuua
gaagcagccaucauuuaaagagugcguaauagcucacuagucgagugaca
cugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggauug
uccuuuggacaaugguaggagagcguucuaagggcguugaagcaugaucg
uaaggacauguggagcgcuuagaagugagaaugccggugugaguagcgaa
agacgggugagaaucccguccaccgauugacuaagguuuccagaggaagg
cucguccgcucuggguuagucggguccuaagcugaggccgacaggcguag
gcgauggauaacagguugauauuccuguaccaccuauaaucguuuuaauc
gauggggggacgcaguaggauaggcgaagcgugcgauuggauugcacguc
uaagcaguaaggcugaguauuaggcaaauccgguacucguuaaggcugag
cugugauggggagaagacauugugucuucgagucguugauuucacacugc
cgagaaaagccucuagauagaaaauaggugcccguaccgcaaaccgacac
agguagucaagaugagaauucuaaggugagcgagcgaacucucguuaagg
aacucggcaaaaugaccccguaacuucgggagaaggggugcucuuuaggg
uuaacgcccagaagagccgcagugaauaggcccaagcgacuguuuaucaa
aaacacaggucucugcuaaaccguaaggugauguauaggggcugacgccu
gcccggugcuggaagguuaagaggagugguuagcuucugcgaagcuacga
aucgaagccccaguaaacggcggccguauaacgguccuaagguagcgaaa
uuccuugucggguaaguuccgacccgcacgaaaggcguaacgauuugggc
acugucucaacgagagacucggugaaaucauaguaccugugaagaugcag
guuacccgcgacaggacggaaagaccccguggagcuuuacuguagccuga
uauugaaauucggcacagcuuguacaggauagguaggagccuuugaaacg
ugagcgcuagcuuacguggaggcgcuggugggauacuacccuagcugugu
uggcuuucuaacccgcaccacuuaucguggugggagacagugucaggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcucaaa
gguucccucagaaugguuggaaaucauucauagaguguaaaggcauaagg
gagcuugacugcgagaccuacaagucgagcagggucgaaagacggacuua
gugauccggugguuccgcauggaagggccaucgcucaacggauaaaagcu
accccggggauaacaggcuuaucucccccaagaguucacaucgacgggga
gguuuggcaccucgaugucggcucaucgcauccuggggcuguagucgguc
ccaaggguugggcuguucgcccauuaaagcgguacgcgagcuggguucag
aacgucgugagacaguucggucccuauccgucgugggcguaggaaauuug
agaggagcuguccuuaguacgagaggaccgggauggacauaccucuggug
uaccaguugucgugccaacggcauagcuggguagcuauguguggacggga
uaagugcugaaagcaucuaagcaugaagccccccucaagaugagauuucc
caacuucgguuauaagaucccucaaagaugaugagguuaauagguucgag
guggaagcauggugacauguggagcugacgaauacuaaucgaucgaagac
uuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6s0x Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.
• Resolution: 2.425 Å
• Binding residue (original residue number in PDB): M12 Q14 P24 D44 K64 S65 K67 K71 G75 R86 E90 K123 K125 G126 F127 G129 K132 S137 M141 S142 H143 G144 H146 F147 H148 R149 G152 S153 M156 A157 S158 D159 A160 S161 R162 V163 R172 T177 T179 Q181 N182 K198 N200 V201 P202 K206 I215 K216
• Binding residue (residue number reindexed from 1): M11 Q13 P23 D43 K63 S64 K66 K70 G74 R85 E89 K122 K124 G125 F126 G128 K131 S136 M140 S141 H142 G143 H145 F146 H147 R148 G151 S152 M155 A156 S157 D158 A159 S160 R161 V162 R171 T176 T178 Q180 N181 K197 N199 V200 P201 K205 I214 K215

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

External links

• PDB: RCSB:6s0x, PDBe:6s0x, PDBj:6s0x
• PDBsum: 6s0x
• PubMed: 31391518
• UniProt: W8U3W0