Structure of PDB 8qcq Chain O Binding Site BS01

Receptor Information

>8qcq Chain O (length=120) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MITKTSKNAARLKRHARVRAKLSGTAERPRLNVFRSNKHIYAQIIDDVNG
VTLASASTLDKDLNVESTGDTSAATKVGELVAKRAAEKGISDVVFDRGGY
LYHGRVKALADAAREAGLKF

Ligand information

>8qcq Chain A (length=2745)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucgaacgagguagaugaagaggucuggaaaggcccgccauagga
gguaacagcccuguagucaaaacuucguucgaguggauccugaguacggc
ggaacacgugaaauuccgucggaauccgggaggaccaucucccaaggcua
aauacucccuagugaccgauagugaaccaguaccgugagggaaaggugaa
aagcaccccggaaggggagugaaagagauccugaaaccgugugccuacaa
guagucagagcccguuaacgggugauggcgugccuuuuguagaaugaacc
ggcgaguuacgaucucgugcaagguuaagcagaagaugcggagccgcagc
gaaagcgagucugaauagggcgcaugaguacguggucguagacccgaaac
caggugaucuacccauguccagggugaaguucagguaacacugaauggag
gcccgaacccacgcacguugaaaagugcggggaugagguguggguagggg
ugaaaugccaaucgaaccuggagauagcugguucucuccgaaauagcuuu
agggcuagccucaagguaagagucuuggagguagagcacugauuggacua
ggggccgguuaccgaauucagucaaacuccgaaugccaaugacuuauccu
ugggagucagacugcgagugauaagauccguagucgaaagggaaacagcc
cagaccgccagcuaaggucccaaaguauacguuaaguggaaaaggaugug
gaguugcuuagacaaccggucgagugacucugcgccgaaaauguaccggg
gcuaaacguaucaccgaagcugcggacuguucgaacagugguaggagagc
guucuaagggcugugaagccagaccggaaggacugguggagcgcuuagaa
gugagaaugccgguaugaguagcgaaagaggggugagaauccccuccacc
gaaugccuaagguuuccugaggaaggcucguccgcucaggguuagucggg
accuaagccgaggccgaaaggcguaggcgauggacaacagguugauauuc
cuguaccaccuccucaccauuugagcaauggggggacgcaggaggauagg
guaagcgcgguauuggauauccgcguccaagcaguuaggcugggaaauag
gcaaauccguuucccaaaggcugagcugugauggcgagcgagcgaaguuc
cugauuccacacugccaagaaaagccucuagcgaggugagaggugcccgu
accgcaaaccgacacagguaggcgaggagagaauccuaaggugaucgaga
gaacucucguuaaggaacucggcaaaaugaccccguaacuucgggagaag
gggugcucuguuagggugcaagcccgagagagccgcagugaauaggccca
ggcgacuguuuagcaaaaacacaggucucugcgaagccguaaggcgaagu
auaggggcugacgccugcccggugcuggaagguuaagaggagcgcuuagc
guaagcgaaggugcgaauugaagccccaguaaacggcggccguaacuaua
acgguccuaagguagcgaaauuccuugucggguaaguuccgacccgcacg
aaaggcgcaacgaucugggcacugucucaacgagagacucggugaaauua
uaguaccugugaagaugcagguuacccgcgacaggacggaaagaccccgu
ggagcuuuacugcagccugauauugaauguugguaauugaccuucuaacc
cgccgcccuuaucgggcggggagacagugucaggugggcaguuugacugg
ggcggucgccuccuaaaagguaacggaggcgcccaaagguucccucagaa
ugguuggaaaucauucgcagaguguaaaggcacaagggagcuugacugcg
agaccuacaagucgagcagggacgaaagucgggcuuagugauccgguggu
uccgcauggaagggccaucgcucaacggauaaaagcuaccccggggauaa
caggcuuaucucccccaagaguccacaucgacggggagguuuggcaccuc
gaugucggcucaucgcauccuggggcuguagucggucccaaggguugggc
uguucgcccauuaaagcgguacgcgagcuggguucagaacgucgugagac
aguucggucccuauccgucgcgggcgcaggaaauuugagaggagcugucc
uuaguacgagaggaccgggauggacgcaccgcugguguaccaguuguucu
gccaagggcaucgcuggguagcuaugugcggacgggauaagugcugaaag
caucuaagcaugaagccccccucaagaugagauuucccauuccgcaagga
aguaagaucccugaaagaugaucagguugauaggucugagguggaagugu
ggcgacacauggagcugacagauacuaaucgaucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qcq Novel arrest peptides induce ribosome stalling by short circuiting the ribosomal peptidyltransferase activity
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): M1 I2 T3 R14 A16 R17 K21 R28 V94 F95 R97 Y102 R114 F120
• Binding residue (residue number reindexed from 1): M1 I2 T3 R14 A16 R17 K21 R28 V94 F95 R97 Y102 R114 F120

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8qcq, PDBe:8qcq, PDBj:8qcq
• PDBsum: 8qcq
• PubMed: 38503735
• UniProt: P46899|RL18_BACSU Large ribosomal subunit protein uL18 (Gene Name=rplR)