Structure of PDB 6wqq Chain C Binding Site BS01

Receptor Information

>6wqq Chain C (length=116) Species: 1280 (Staphylococcus aureus)

PRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRR
QRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAIS
DEKAFAQLVTKAKDAL

Ligand information

>6wqq Chain 1 (length=2698)

uaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgaugaa
ggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuugau
ccagagauuuccgaauggggaaacccagcaugaguuaugucauguuaucg
auaugugaauacauagcauaucagaaggcacacccggagaacugaaacau
cuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcg
agcgaaacgggaagagcccaaaccaacguugggguuguaggacacucuag
uuacaaaggacgacauuagacgaaucaucuggaaagaugaaucaaagaag
guaauaauccuguagucgaaaauguugucucucuugaguggauccugagu
acgacggagcacgugaaauuccgucggaaucugggaggaccaucuccuaa
ggcuaaauacucucuagugaccgauagugaaccaguaccgugagggaaag
gugaaaagcaccccggaaggggagugaaauagaaccugaaaccgugugcu
uacaaguagucagagcccguuaaugggugauggcgugccuuuuguagaau
gaaccggcgaguuacgauuugaugcaagguuaagcaguaaauguggagcc
guagcgaaagcgagucugaauagggcguuuaguauuuggucguagacccg
aaaccaggugaucuacccuuggucagguugaaguucagguaacacugaau
ggaggaccgaaccgacuuacguugaaaagugagcggaugaacugagggua
gcggagaaauuccaaucgaaccuggagauagcugguucucuccgaaauag
cuuuagggcuagccucaagugaugauuauuggagguagagcacuguuugg
acgagcgaauucagacaaacuccgaaugccaauuaauuuaacuugggagu
cagaacaugggugauaagguccguguucgaaagggaaacagcccagacca
ccagcuaaggucccaaaauauauguuaaguggaaaaggauguggcguugc
cacagagugacacugcgccgaaaauguaccggggcuaaacauauuaccga
agcuguggauuguccuuuggacaaugguaggagagcguucuaagggcguu
gaagcaugaucguaaggacauguggagcgcuuagaagugagaaugccggu
gugaguagcgaaagacgggugagaaucccguccaccgauugacuaagguu
uccagaggaaggcucguccgcucuggguuagucggguccuaagcugaggc
cgacaggcguaggcgauggauaacagguugauauuccuguaccaccuaua
aucguaucgauggggggacgcaguaggauaggcgaagcgugcgauuggau
ugcacgucuaagcaguaaggcuguccgguagcugagcugugauggggaga
agaccuucgagucguugauuucacacugccgagaaaagccucuagauaga
aaauaggugcccguaccgcaaaccgacacagguagucaagaugagaauuc
uaaggugagcgagcgaacucucguuaaggaacucggcaaaaugaccccgu
aacuucgggagaaggggugcucuuuaggguuaacgcccagaagagccgca
gugaauaggcccaagcgacuguuuaucaaaaacacaggucucugcuaaac
cguaaggugauguauaggggcugacgccugcccagugcuggaagguuaag
aggagugguuagcuucugcgaagcuacgaaucgaagccccaguaaacggc
ggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaagu
uccgacccgcacgaaaggcguaacgauuugggcacugucucaacgagaga
cucggugaaaucauaguaccugugaagaugcagguuacccgcgacaggac
ggaaagaccccguggagcuuuacuguagccugauauugaaauucggcuuu
cuaacccgcaccacuuaucguggugggagacagugucaggcgggcaguuu
gacuggggcggucgccuccuaaaagguaacggaggcgcucaaagguuccc
ucagaaugguuggaaaucauucauagaguguaaaggcauaagggagcuug
acugcgagaccuacaagucgagcagggucgaaagacggacuuagugaucc
ggugguuccgcauggaagggccaucgcucaacggauaaaagcuaccccgg
ggauaacaggcuuaucucccccaagaguucacaucgacggggagguuugg
caccucgaugucggcucaucgcauccuggggcuguagucggucccaaggg
uugggcuguucgcccauuaaagcgguacgcgagcuggguucagaacgucg
ugagacaguucggucccuauccgucgugggcguaggaaauuugagaggag
cuguccuuaguacgagaggaccgggauggacauaccucugguguaccagu
ugucgugccaacggcauagcuggguagcuauguguggacgggauaagugc
ugaaagcaucuaagcaugaagccccccucaagaugagauuucccaacuuc
gguuauaagaucccucaaagaugaugagguuaauagguucgagguggaag
cauggugacauguggagcugacgaauacuaaucgaucgaagacuuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wqq Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 V4 K5 T8 T10 R11 R13 R14 K15 G23 Y24 F25 G26 S27 T30 L31 K33 K36 Q37 Q38 K41 S42 Y45 R48 D49 R50 R51 R53 K54 R55 F57 R58 K59 R70 Y76 S77 N81 K84 N91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 V3 K4 T7 T9 R10 R12 R13 K14 G22 Y23 F24 G25 S26 T29 L30 K32 K35 Q36 Q37 K40 S41 Y44 R47 D48 R49 R50 R52 K53 R54 F56 R57 K58 R69 Y75 S76 N80 K83 N90 R91 K92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6wqq, PDBe:6wqq, PDBj:6wqq
• PDBsum: 6wqq
• PubMed: 32566908
• UniProt: Q2FXQ1|RL20_STAA8 Large ribosomal subunit protein bL20 (Gene Name=rplT)