Structure of PDB 6xa1 Chain SI Binding Site BS01

Receptor Information

>6xa1 Chain SI (length=197) Species: 9606 (Homo sapiens)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKEEEILNKKRSKKIQKKYDERKKNAKIS
SLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARK

Ligand information

>6xa1 Chain L5 (length=3510)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgggggcgcgggacaugugg
cguacggaagacccgcuccccggggggcccaaguccuucugaucgaggcc
ccguggacggugugaggccgguagcggcccccgggcccgggucuucccgg
agucggguugcuugggaaugcagcccaaagcgggugguaaacuccaucua
aggcuaaauaccggcacgagaccgauagucaacaaguaccguaagggaaa
guugaaaagaacuuugaagagagaguucaagagggcgugaaaccguuaag
agguaaacgggugggguccgcgcaguccgcccggaggauucaacccggcg
gcggguccggccgggcggaucugggaccguccccggccgccgccgggcgc
auuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaagg
cccggcggggaagguggcucggccgaguguuacagcccccccggcagcag
cacucgccgaaucccggggccgagggagcgagacccgucgccgcgcucuc
cccccugggggggccgggccaccccucccacggcgcgaccgcuggggcgg
acuguucccagugcgccccgggcgggucgcgccgucgggcccggggggcc
acgcgcgcgucccgggacggcggagcgagcgcacggggucggcggcgacg
ucggcuacccacccgacccgucuugaaacacggaccaaggagucuaacac
gugcgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggug
aaggccggccgaggugggaucccgaggccucuccaguccgccgagggcgc
accaccggcccgucucgcccgccgcgccggggagguggagcacgagcgca
cguguuaggacccgaaagauggugaacuaugccugggcagggcgaagcca
gaggaaacucugguggagguccguagcgguccugacgugcaaaucggucg
uccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugg
uucccuccgaaguuucccucaggauagcuggcgcucucgcagacccgacg
cccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuugguca
accuauucucaaacuuuaaauggguaagaagcccggcucgcuggcgugga
gccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaac
uggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacg
cucaucagaccccagaaaagguguugguugauauagacagcaggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccugccga
aucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccg
gccgucgccggcagucgagaguggacgggagcggcgggccggagccccgc
ggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagc
cuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggua
guagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuc
caugugaacagcaguugaacaugggucagucgguccugagagaugggcga
gcgccguuccgaagggacgggcgauggccuccguugcccucggccgaucg
aaagggagucggguucagauccccgaauccggaguggcggagaugggcgc
cgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggg
agccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaa
uggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguucc
ggcggcguccggugagcucucgcuggcccuugaaaauccgggggagaggg
uguaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggu
gaacagccucuggcauguuggaacaauguagguaagggaagucggcaagc
cggauccguaacuucgggauaaggauuggcucuaagggcugggucggucg
cggccggcgccuagcagccgacuuagaacuggugcggaccaggggaaucc
gacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugac
gcgaugugauuucugcccagugcucugaaugucaaagugaagaaauucaa
ugaagcgcggguaaacggcgggaguaacuaugacucucuuaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuc
ccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcu
uggcggaaucagcggggaaagaagacccuguugagcuugacucuagucug
gcacggugaagagacuuuuuucacugacccggugaggcgggggggcgagc
ucucgcuucuggcgccaagcgcccggcgccgggcgcgacccgcuccgggg
acagugccagguggggaguuugacuggggcgguacaccugucaaacggua
acgcagguguccuaaggcgagcucagggaggacagaaaccucccguggag
cagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagacc
gugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcagga
ggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgu
ucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauu
gugaagcagaauucaccaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacagcgccgcggagccucgguuggccucggauagccggucc
cggguccggugcggagugcccuucguccugggaaacggggcgcggccgga
gaggcggccgcccccucgcccgucacgcaccgcacguucguggggaaccu
ggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguacg
uagcagagcagcucccucgcugcgaucuauugaaagucagcccucgacac
aaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xa1 Selective inhibition of human translation termination by a drug-like compound.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): R77 N88 R92 T93 D105
• Binding residue (residue number reindexed from 1): R76 N87 R91 T92 D104

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xa1, PDBe:6xa1, PDBj:6xa1
• PDBsum: 6xa1
• PubMed: 33009412
• UniProt: P62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)