Structure of PDB 8qbt Chain y Binding Site BS01

Receptor Information

>8qbt Chain y (length=80) Species: 679895 (Escherichia coli BW25113)

KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNEC
GIGDVVEIRECRPLSKTKSWTLVRVVEKAV

Ligand information

>8qbt Chain i (length=1539)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuu
cgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaac
aagguaaccguaggggaaccugcgguuggaucaccuccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qbt Novel arrest peptides induce ribosome stalling by short circuiting the ribosomal peptidyltransferase activity
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): K4 R6 K16 M17 E18 K19 R27 I33 K36 F37 K39 R40 T41 T42 K43 L44 H45 E63 R65 P66 S68 K69 T70 K71 W73
• Binding residue (residue number reindexed from 1): K1 R3 K13 M14 E15 K16 R24 I30 K33 F34 K36 R37 T38 T39 K40 L41 H42 E60 R62 P63 S65 K66 T67 K68 W70

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qbt, PDBe:8qbt, PDBj:8qbt
• PDBsum: 8qbt
• PubMed: 38503735
• UniProt: P0AG63|RS17_ECOLI Small ribosomal subunit protein uS17 (Gene Name=rpsQ)