Structure of PDB 6s13 Chain C Binding Site BS01

Receptor Information

>6s13 Chain C (length=274) Species: 1280 (Staphylococcus aureus)

AIKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTV
RHHGGGHKRQYRVIDFKRNKDGINAKVDSIQYDPNRSANIALVVYADGEK
RYIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKG
GQIARSAGASAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHE
LVNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRPSPMSPWG
KPTLGKKTRRGKKSSDKLIVRGRK

Ligand information

>6s13 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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<<.<<.............>>.>>.>>.>>.....<<<<......<<....
>>.......>>>>.....................<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<
<<<<<............................<<<...<<<<<......
>>>>>((......<<<.....))>>>...>>>..................
...>>..>>>>.....<<<<<<<<.........>>>>>>>>......<<<
<<..<<<<>>>>>..))).......].>>>>>>>.)))............
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}....>>>>>>>>>>........<<<<..<<<<......>>>>..>>>>.
..<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<
<.....>>>...>>>...<<....>>..<<<<.....>>>>.....>>>>
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....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>>
>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<
<...........<<...................<..<..<<...<<....
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.<<<<<<.......>>>>>><<<<....<<<<<.<<<..<<<<<<...<<
.....>>.>>>>>>....((<<<<<<<...<<<...<<<....>>>...>
>>...>>>..<<<<<........>>>>>))<<<<<<............<<
....<<<....<<<<<.<.<..............................
..........<<<.<<<<<<..<.......>.>>>>>>......>>>...
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.........>>>...>>.......>>>>>>>>>>.>>>.....<<.....
.>>>>>>>.<<<.......>>>..>>>>..<<<<....<<<<<<<<.<<.
..............<<<<<...............>>>>><<<<<...<<.
.......>>...>>>>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.
.<<..<<<<<<<..<<<...<<............................
.>>...>>>>>>>>..>>>>.<<<<.......>>>>..............
......<<<<<<.....>>>>>>..........>>>>>..>>.>>>>>>>
.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>
>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<<<..<<<<<<
<<<.<<<<...<.....<<..............<<<..<<..........
.<<<<....>>>>........>>............>>>.....>>.....
>...>>>>....<<.<<<<<<.....>>>>>>>>.....>>>>>>>>>..
.>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...
<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>....>>
>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))]
......<<<<<<..((..>>>>..)).>>>>>>.............>>>>
..]]>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>
>....>>>.>.......<.<<<.<<<<<<..<<<<<<<<<......>>>>
>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>..>....<
<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<......>>>>>..>>>>>...>>>>.>>>>>...<<<.
..<....................>....>>>.>>>>.......>>>>>>>
..<......>.....<<<<<<<<<.......>>>>>....<<<<<<<<.<
<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>>
.>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6s13 Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.
• Resolution: 3.58 Å
• Binding residue (original residue number in PDB): T10 N11 R13 R14 N15 T27 K31 L37 K40 R43 N45 Q46 K48 L49 T50 R52 H53 H54 H58 K59 Q61 Y62 R63 F67 Y83 P85 R87 D98 G99 E100 K101 K147 G149 K150 Q153 I154 A155 R156 S157 A158 G159 L176 R177 R182 L198 H200 E201 N204 V205 G206 K207 G209 R210 S211 R212 W213 R217 P218 T219 V220 R221 S223 V224 M225 N226 N228 D229 H232 G235 E236 R238 P240 I241 G242 R243 S248 W250 K252 T254 L255 G256 K257 K258 T259 R260 K263 K268
• Binding residue (residue number reindexed from 1): T9 N10 R12 R13 N14 T26 K30 L36 K39 R42 N44 Q45 K47 L48 T49 R51 H52 H53 H57 K58 Q60 Y61 R62 F66 Y82 P84 R86 D97 G98 E99 K100 K146 G148 K149 Q152 I153 A154 R155 S156 A157 G158 L175 R176 R181 L197 H199 E200 N203 V204 G205 K206 G208 R209 S210 R211 W212 R216 P217 T218 V219 R220 S222 V223 M224 N225 N227 D228 H231 G234 E235 R237 P239 I240 G241 R242 S247 W249 K251 T253 L254 G255 K256 K257 T258 R259 K262 K267

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6s13, PDBe:6s13, PDBj:6s13
• PDBsum: 6s13
• PubMed: 31391518
• UniProt: B3VKN3