Structure of PDB 6wqq Chain F Binding Site BS01

Receptor Information

>6wqq Chain F (length=87) Species: 1280 (Staphylococcus aureus)

RDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASV
NIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSDDLF

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): T13 K15 K24 R32 N34 K35 T36 N54 M56 N57 Y58 K59 K61 R64 M65 Y68 G70 N73 R76
• Binding residue (residue number reindexed from 1): T10 K12 K21 R29 N31 K32 T33 N51 M53 N54 Y55 K56 K58 R61 M62 Y65 G67 N70 R73

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: Q2FW08|RL23_STAA8 Large ribosomal subunit protein uL23 (Gene Name=rplW)