Structure of PDB 8qcq Chain F Binding Site BS01

Receptor Information

>8qcq Chain F (length=178) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

NRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAID
SAVEELTFIAGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLD
KLISVSLPRVRDFRGVSKKSFDGRGNYTLGIKEQLIFPEIDYDKVTKVRG
MDIVIVTTANTDEEARELLTQVGMPFQK

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): K33 V35 N37 M38 G39 G41 T68 K71 I74 G76 F77 I85 K88 S121 D123 R125 N127 T129 G131 I132 G151 M152 D153 V155
• Binding residue (residue number reindexed from 1): K32 V34 N36 M37 G38 G40 T67 K70 I73 G75 F76 I84 K87 S120 D122 R124 N126 T128 G130 I131 G150 M151 D152 V154

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• 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: P12877|RL5_BACSU Large ribosomal subunit protein uL5 (Gene Name=rplE)