Structure of PDB 6wqn Chain X Binding Site BS01

Receptor Information

>6wqn Chain X (length=144) Species: 1280 (Staphylococcus aureus)

KLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFE
GGQLPLFRRLPKRGFTNINRKEYAIVNLDQLNKFEDGTEVTPALLVESGV
VKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEV

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): H4 L6 G11 S12 R13 K14 R16 R18 G20 R21 A24 G28 K29 T30 G32 R33 G34 K36 Q38 K39 R41 S42 G43 R47 F50 G52 G53 Q54 L55 R60 P62 K63 R64 G65 F66 N68 N70 R71 I76 N78 K103 K110 L112 N114 S129 A130
• Binding residue (residue number reindexed from 1): H3 L5 G10 S11 R12 K13 R15 R17 G19 R20 A23 G27 K28 T29 G31 R32 G33 K35 Q37 K38 R40 S41 G42 R46 F49 G51 G52 Q53 L54 R59 P61 K62 R63 G64 F65 N67 N69 R70 I75 N77 K102 K109 L111 N113 S128 A129

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

External links

• PDB: RCSB:6wqn, PDBe:6wqn, PDBj:6wqn
• PDBsum: 6wqn
• PubMed: 32566908
• UniProt: P0A0F8|RL15_STAA8 Large ribosomal subunit protein uL15 (Gene Name=rplO)