Structure of PDB 8qcq Chain 0 Binding Site BS01

Receptor Information

>8qcq Chain 0 (length=55) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

AVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNG
KDINV

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): A2 V3 P4 F5 R6 R7 T8 S9 K10 M11 K12 K13 R14 L15 R16 R17 T18 H19 F20 K21 T28 K37 S39 H40 R41 Y49 N50
• Binding residue (residue number reindexed from 1): A1 V2 P3 F4 R5 R6 T7 S8 K9 M10 K11 K12 R13 L14 R15 R16 T17 H18 F19 K20 T27 K36 S38 H39 R40 Y48 N49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qcq, PDBe:8qcq, PDBj:8qcq
• PDBsum: 8qcq
• PubMed: 38503735
• UniProt: O34687|RL32_BACSU Large ribosomal subunit protein bL32 (Gene Name=rpmF)