Structure of PDB 8wkp Chain S10P Binding Site BS01

Receptor Information

>8wkp Chain S10P (length=100) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

TKARIRLWSSNIDSLNFVVNQIRNMAQKTGIQVSGPIPLPTTRMEVPVMR
LPHGEGKKKWEHWEMKVHKRIIDIAADERVMRQLMRVRVPDDVYIEIELI

Ligand information

>8wkp Chain A16S (length=1325)

auuccgguugauccugccggacccgaccgcuaucgggguagggauaagcc
augggagucuuacacucccggguaagggaguguggcggacggcugaguaa
cacguggcuaaccuacccucgggacggggauaaccccgggaaacugggga
uaauccccgauagggaaggaguccuggaaugguuccuucccuaaagggcu
auaggcuauuucccguuuguagcgcccgaggauggggcuacggcccauca
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: 8wkp Structural basis of translation inhibition by a valine tRNA-derived fragment
• Resolution: 4.62 Å
• Binding residue (original residue number in PDB): R6 I14 G37 P38 I39 P40 L41 T44 R45 M46 R52 L53 H55 G56 E57 G58 K59 K61 W62 H64 H70 I73 D75 E100
• Binding residue (residue number reindexed from 1): R4 I12 G35 P36 I37 P38 L39 T42 R43 M44 R50 L51 H53 G54 E55 G56 K57 K59 W60 H62 H68 I71 D73 E98

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8wkp, PDBe:8wkp, PDBj:8wkp
• PDBsum: 8wkp
• PubMed: 38599770
• UniProt: P17199|RS10_SULAC Small ribosomal subunit protein uS10 (Gene Name=rps10)