Structure of PDB 6wqn Chain V Binding Site BS01

Receptor Information

>6wqn Chain V (length=143) Species: 1280 (Staphylococcus aureus)

RQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDT
GDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPERL
IENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELR

Ligand information

>6wqn Chain 1 (length=2687)

uaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgaugaa
ggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuugau
ccagagauuuccgaauggggaaacccagcaugaguuaugucauguuaucg
auaugugaauacauagcauaucagaaggcacacccggagaacugaaacau
cuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcg
agcgaaacgggaagagcccaaaccaacguugggguuguaggacacucuag
uuacaaaggacgacauuagacgaaucaucuggaaagaugaaucaaagaag
guaauaauccuguagucgaaaauguugucucucuugaguggauccugagu
acgacggagcacgugaaauuccgucggaaucugggaggaccaucuccuaa
ggcuaaauacucucuagugaccgauagugaaccaguaccgugagggaaag
gugaaaagcaccccggaaggggagugaaauagaaccugaaaccgugugcu
uacaaguagucagagcccguuaaugggugauggcgugccuuuuguagaau
gaaccggcgaguuacgauuugaugcaagguuaagcaguaaauguggagcc
guagcgaaagcgagucugaauagggcguuuaguauuuggucguagacccg
aaaccaggugaucuacccuuggucagguugaaguucagguaacacugaau
ggaggaccgaaccgacuuacguugaaaagugagcggaugaacugagggua
gcggagaaauuccaaucgaaccuggagauagcugguucucuccgaaauag
cuuuagggcuagccucaagugaugauuauuggagguagagcacuguuugg
acgagcgaauucagacaaacuccgaaugccaauuaauuuaacuugggagu
cagaacaugggugauaagguccguguucgaaagggaaacagcccagacca
ccagcuaaggucccaaaauauauguuaaguggaaaaggauguggcguaca
gagugacacugcgccgaaaauguaccggggcuaaacauauuaccgaagcu
guggauuguccuuuggacaaugguaggagagcguucuaagggcguugaag
caugaucguaaggacauguggagcgcuuagaagugagaaugccgguguga
guagcgaaagacgggugagaaucccguccaccgauugacuaagguuucca
gaggaaggcucguccgcucuggguuagucggguccuaagcugaggccgac
aggcguaggcgauggauaacagguugauauuccuguaccaccuauaaucg
uaucgauggggggacgcaguaggauaggcgaagcgugcgauuggauugca
cgucuaagcaguaaggcugcgguagcugagcugugauggggagaagaccu
ucgagucguugauuucacacugccgagaaaagccucuagauagaaaauag
gugcccguaccgcaaaccgacacagguagucaagaugagaauucuaaggu
gagcgagcgaacucucguuaaggaacucggcaaaaugaccccguaacuuc
gggagaaggggugcucuuuaggguuaacgcccagaagagccgcagugaau
aggcccaagcgacuguuuaucaaaaacacaggucucugcuaaaccguaag
gugauguauaggggcugacgccugcccagugcuggaagguuaagaggagu
gguuaggcgaagcuacgaaucgaagccccaguaaacggcggccguaacua
uaacgguccuaagguagcgaaauuccuugucggguaaguuccgacccgca
cgaaaggcguaacgauuugggcacugucucaacgagagacucggugaaau
cauaguaccugugaagaugcagguuacccgcgacaggacggaaagacccc
guggagcuuuacuguagccugauauugaaauucggcuuucuaacccgcac
cacuuaucguggugggagacagugucaggcgggcaguuugacuggggcgg
ucgccuccuaaaagguaacggaggcgcucaaagguucccucagaaugguu
ggaaaucauucauagaguguaaaggcauaagggagcuugacugcgagacc
uacaagucgagcagggucgaaagacggacuuagugauccggugguuccgc
auggaagggccaucgcucaacggauaaaagcuaccccggggauaacaggc
uuaucucccccaagaguucacaucgacggggagguuuggcaccucgaugu
cggcucaucgcauccuggggcuguagucggucccaaggguugggcuguuc
gcccauuaaagcgguacgcgagcuggguucagaacgucgugagacaguuc
ggucccuauccgucgugggcguaggaaauuugagaggagcuguccuuagu
acgagaggaccgggauggacauaccucugguguaccaguugucgugccaa
cggcauagcuggguagcuauguguggacgggauaagugcugaaagcaucu
aagcaugaagccccccucaagaugagauuucccaacuucgguuauaagau
cccucaaagaugaugagguuaauagguucgagguggaagcauggugacau
guggagcugacgaauacuaaucgaucgaagacuuaau

.<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<<......
<<<<<<.[...((.>>>.....<<<<<<<..<<<))...].>>>.....>
>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<<
<<<<<...........>>>>>>.>>.>>....<<<<<......<......
>.......>>>>.>.........<<....>>..<<<<<......<<....
.>>.....>>>>>..<<<....<<......>>.......<<<.......<
........<<<<<<<<<.<<<...<<<<<......>>>>>((......<<
<.....))>>>...>>>...>>>>>>>>.>.>..........>>>.....
.<<<<<<<<.........>>>>>>>>......<<<<<..<<<<>>>>>..
>>>......>>.>>>>>>>.>>...............<<....>>....>
>.........<<<<....>>>>..................>>>>>>>>>>
>.......<<<<..<<<<......>>>>..>>>>...<.<........>.
>.<<<<<<....<<<<<<<.<<<<<..<<<...<<<.....>>>...>>>
...<<....>>..<<<<.....>>>>.....>>>>>.>>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<........>>>>>
.....>>>...<<<.<<<<<........>>>>>>>>....>>>>>>>>>.
..<<<.....>>>......>>>>>>...>..>.>>..<<<<<<....<<<
<<....>>>>><<<<<<<<<...<<<<<<<<<......<<...<<<<<<<
..........>>>>>>>..>>.......>>>>.>>>>>..>>>>>>>.>>
..<<<<<<<<<<......>>>>>>>>>>....<<<......>>>...<<<
<.<<<...<<<(((.....<<<<<<...........<<..<<<<.<<...
.....>>.>>>>.>>...........))).....>>>>>>.>>>...>>>
>>>><<<<<<.....>>>>>>....>>>>>><.<<<<<<<.<.......<
<<<<.<<....>>.>>>>>....>.>>>>>>>..>.....>>>>>><...
...<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<...
.>>>...>>>...>>...<<<<<........>>>>>))<<<<<<......
..<<...<<<<....<<<<...<<...<......<<<.........>>>.
..<.....<<<...<<.........>>...>>>......>..........
.........>....>>...>>>>.........>>>.>.>>.......>>>
>>>>>>>..>>.....<<......>>>>>>>.<<<<....>.>>>..>>>
>..<<<<....<<<<<<<<.<<.........<.....<<<<<........
.......>>>>><<<<<<<.<<<<....>>>>.>>>>>>>..........
..<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>
>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<<..<<...<<
<<<........>>>>>...>>..>>>>>>>>>..>>>>><<<<<<.....
..>>>>>>........<...........<<<<<<.....>>>>>>.....
>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>.>.....
>.....<<<<<........>>>>>..<<<<<<<<.<<<.<<......<<<
<.<<<<<<..<<<<<.<<<<<<<<<.<<<<......>>>>....<<.<<<
<<<.....>>>>>>>>.....>>>>>>>>>..>>>>>..<<<<.....>>
>><<<<<<...........>>>>>>..<<...<<<<<<<......<<<..
.....>>>........<<.[.(((>>....>>>>>>>...<<<<..<<<.
.....>>>..>>>>.<<<....>>>.>>)))]......<<<<<<.<<<..
>>>>..>>>>>>>>>.............>>>>..>>>>>>.......<<<
<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<
<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....
>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>
....>>..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<....
...........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<......
>>>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<<<..........
.>>>>>...>>>>.>>>>.......>>>>>>>.<<<....>>>....<<<
<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>
>>...>>>..>>>>>.>>>...>>>>....>>>>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wqn Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R2 T4 N8 L26 G27 R28 S31 R38 K40 H48 T66 K69 K73 Y75 Y76 R77 H78 S79 H81 P82 G83 K86 E103 S105 M109 R114 L115 K121 H133 A135 Q136 Q137
• Binding residue (residue number reindexed from 1): R1 T3 N7 L25 G26 R27 S30 R37 K39 H47 T65 K68 K72 Y74 Y75 R76 H77 S78 H80 P81 G82 K85 E102 S104 M108 R113 L114 K120 H132 A134 Q135 Q136

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6wqn, PDBe:6wqn, PDBj:6wqn
• PDBsum: 6wqn
• PubMed: 32566908
• UniProt: Q2FW38|RL13_STAA8 Large ribosomal subunit protein uL13 (Gene Name=rplM)