Structure of PDB 8qcq Chain W Binding Site BS01

Receptor Information

>8qcq Chain W (length=85) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

ASKKGVGSTKNGRDSEAKRLGAKRADGQFVTGGSILYRQRGTKIYPGENV
GRGGDDTLFAKIDGTVKFERFGRDRKKVSVYPVAQ

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): A10 S11 K12 S17 T18 N20 R22 D23 S24 E25 A26 K27 R28 L29 K32 R33 A34 D35 G36 Q37 G41 G42 S43 I44 Y46 R47 R49 G50 T51 K52 Y54 G62 G63 D64 D65 T66 F68 F77 R84 K85
• Binding residue (residue number reindexed from 1): A1 S2 K3 S8 T9 N11 R13 D14 S15 E16 A17 K18 R19 L20 K23 R24 A25 D26 G27 Q28 G32 G33 S34 I35 Y37 R38 R40 G41 T42 K43 Y45 G53 G54 D55 D56 T57 F59 F68 R75 K76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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: P05657|RL27_BACSU Large ribosomal subunit protein bL27 (Gene Name=rpmA)