Structure of PDB 6s13 Chain J Binding Site BS01

Receptor Information

>6s13 Chain J (length=146) Species: 1280 (Staphylococcus aureus)

MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGF
EGGQLPLFRRLPKRGFTNINRKEYAIVNLDQLNKFEDGTEVTPALLVESG
VVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI

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

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

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): L3 H4 K7 S12 R13 K14 E15 R16 R18 G20 R21 G22 A24 G28 K29 T30 S31 G32 R33 K36 G37 Q38 K39 R41 S42 G43 V46 R47 F50 E51 G52 G53 Q54 R59 R60 P62 K63 R64 G65 F66 N68 R71 E73 K103 K110 L112 G113 N114
• Binding residue (residue number reindexed from 1): L3 H4 K7 S12 R13 K14 E15 R16 R18 G20 R21 G22 A24 G28 K29 T30 S31 G32 R33 K36 G37 Q38 K39 R41 S42 G43 V46 R47 F50 E51 G52 G53 Q54 R59 R60 P62 K63 R64 G65 F66 N68 R71 E73 K103 K110 L112 G113 N114

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:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6s13, PDBe:6s13, PDBj:6s13
• PDBsum: 6s13
• PubMed: 31391518
• UniProt: A0A077UGA7