Structure of PDB 8wq4 Chain AS5P Binding Site BS01

Receptor Information

>8wq4 Chain AS5P (length=204) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

EDWKPRTKVGQLIKEGKINSMKELFERNLPIVEPEIVDVLLPKLRYDIVD
IGIVQKQTDAGELSRYKVLIVMGNMDGYISYGTGKAKQLRVAIQKAIRDA
KMRIIPVRRGCGSWECTCGESHSLPFIVSGKAGSVEVTLLPAPKGTGLVV
GSVLKTFLSLAGLKDVWSRTKGSTYTHENFIKAAYIALYNTYRFVTPVDW
GRMK

Ligand information

>8wq4 Chain A16S (length=1325)

auuccgguugauccugccggacccgaccgcuaucgggguagggauaagcc
augggagucuuacacucccggguaagggaguguggcggacggcugaguaa
cacguggcuaaccuacccucgggacggggauaaccccgggaaacugggga
uaauccccgauagggaaggaguccuggaaugguuccuucccuaaagggcu
auagguauuucccguuuguagccgcccgaggauggggcuacggcccauca
ggcugucggugggguaaaggcccaccgaaccuauaacggguaggggccgu
ggaagcgggagccuccaguugggcacugagacaagggcccaggcccuacg
gggcgcaccaggcgcgaaacguccccaaugcgcgaaagcgugagggcgcu
accccgagugccuccgcaggaggcuuuuccccgcucuaaaaaggcggggg
aauaagcggggggcaagucuggugucagccgccgcgguaauaccagcucc
gcgaguggucggggugauuacugggccuaaagcgccuguagccggcccac
caagucgccccuuaaaguccccggcucaaccggggaacugggggcgauac
uggugggcuagggggcgggagaggcgggggguacucccggaguaggggcg
aaauccuuagauaccgggaggaccaccaguggcggaagcgccccgcuaga
acgcgcccgacggugagaggcgaaagccgggggucccggcuguaaacgau
gcgggcuaggugucgaguaggcuuagagccuacucggugccgcagggaag
ccguuaagcccgccgccuggggaguacggucgcaagacugaaacuuaaag
gaauuggcgggggagcaccacaagggguggaaccugcggcucaauuggag
ucaacgccuggaaucuuaccggggagaccgcaguaugacggccaggcuaa
cgaccuugccugacucgcggagaggaggugcauggccgucgccagcucgu
guugugaaauguccgguuaaguccggcaacgagcgagacccccaccccua
guugguauucuggacuccgguccagaaccacacuagggggacugccggcg
uaagccggaggaaggagggggccacggcaggucagcaugccccgaaaccg
ggccgcacgcggguuacaauggcagggacaacgggaugcuaccucgaaag
ggggagccaauccuuaaacccugccgcaguugggaucgagggcugaaacc
cgcccucgugaacgaggaaucccuaguaaccgcgggucaacaacccgcgg
ugaauacgucccugcuccuugcaca

...<<<<<...((((>>>>>.<<<<<<<<......<<<.<<......<<<
.<<<...<...<.<<<<<........>>>>>.>.>.......<<..<...
..<<<<<<<..<<...<<<<<<<.<<<<<....<<<<........>>>>.
....>>>>>....<<.<<<.<<<.......>>>>>.>>.>......<<<<
<<.<...........>.>>>>>>.>>>>>>>..>>>>>>>>>.<<<....
<<....<<<<<<<.......>>>>>>>..>>......>>>....<<<<<<
....>>>>...>>..>>>.<<<<<............>>>>>.<<<<<..>
>>>>...>>>>>>.........<<<....<<<<....>>>>..>>>..>>
..>>>....<<<<<.....>>>>>...<<<<<<<.........>>>>>>>
.....<<<<<((......<<<<.....<<..))>>.......>>>>.>>>
>>...>>>>>>>>..........<<<((.....<<<<...<<<.<<<<<<
<.<<..<<<<<......<<<<<<<.....>>>>>>>....>>>>>....>
>>>>>>>>...<<<<<<.....<<<<<<<<<..<<<<<<<....<<....
....>>.......>>>>>>>..>>.......<<....>>.>>>>>>>...
.>>>.>>>...>>>...>>>>....<<<<<.....>>>>>..........
<<<<<<..<<<.<<<<<<<<<<.....>>>>>>>>>>.>>>...<<..))
>>.....>>>>>>.>>>..<<.....<<<<<....>>>>>...>>...))
))..........<<<<<..<<.<<<<<...<<<<<<<.<<......<...
.......>..........<<<..........<........<<.<<<....
...>>>.>>.....>........<<.<<....<<<<<<<.....<<<<<.
<<......>>..<<<<......>>>>...>>>>>....<<<<<.<<<<.<
<.........<<<<<....>>>>>........>>.>>>>.....<<<<<.
...>>>>>........>>>>>.....>>.>>>...>>..>>>>.....>>
>...>>..>>>>>>>.....<<<<<<<......<<..<<..<<<......
>>>..>>....>>.....>>>>>>>.............<<<<<.......
.>>>>>.............>>>>>....<<<<<<<<.......>>>>>>>
>......>>...>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8wq4 Structural basis of translation inhibition by a valine tRNA-derived fragment
• Resolution: 4.53 Å
• Binding residue (original residue number in PDB): Q70 K71 Q72 T73 D74 T98 S149 T161 V165 G166 S167 W182 K186 T189 Y190 N194 K197
• Binding residue (residue number reindexed from 1): Q55 K56 Q57 T58 D59 T83 S134 T146 V150 G151 S152 W167 K171 T174 Y175 N179 K182

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8wq4, PDBe:8wq4, PDBj:8wq4
• PDBsum: 8wq4
• PubMed: 38599770
• UniProt: O05641|RS5_SULAC Small ribosomal subunit protein uS5 (Gene Name=rps5)