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Structure of PDB 8yoo Chain SI Binding Site BS01

Receptor Information
>8yoo Chain SI (length=206) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARKG
Ligand information
>8yoo Chain L5 (length=3670) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcuggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccga
agagggggacggcggagcgagcgcacggggucggcggcgacgucggcuac
ccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcga
gucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgg
cgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgagg
gcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcgccacgcaguuuuauccgguaaagcgaaugauuagaggucuuggg
gccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccg
gcucgcuggcguggagccgggcguggaaugcgagugccuagugggccacu
uuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaagg
cgcccgaugccgacgcucaucagaccccagaaaagguguugguugauaua
gacagcaggacgguggccauggaagucggaauccgcuaaggaguguguaa
caacucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcg
ucgggcccauacccggccgucgccggcagucgagaguggacgggagcggc
ggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgcugc
ggugagccuugaagccuagggcgcgggcccggguggagccgccgcaggug
cagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccga
aguggagaaggguuccaugugaacagcaguugaacaugggucagucgguc
cugagagaugggcgagcgccguuccgaagggacgggcgauggccuccguu
gcccucggccgaucgaaagggagucggguucagauccccgaauccggagu
ggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauccc
ggagaagccggcgggagccccggggagaguucucuuuucuuugugaaggg
cagggcgcccuggaauggguucgccccgagagaggggcccgugccuugga
aagcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaa
auccgggggagaggguguaaaucucgcgccgggccguacccauauccgca
gcaggucuccaaggugaacagccucuggcauguuggaacaauguagguaa
gggaagucggcaagccggauccguaacuucgggauaaggauuggcucuaa
gggcugggucggucgcggccggcgccuagcagccgacuuagaacuggugc
ggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggccc
gcggcggguguugacgcgaugugauuucugcccagugcucugaaugucaa
agugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacu
cucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaau
ggaugaacgagauucccacugucccuaccuacuauccagcgaaaccacag
ccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguugag
cuugacucuagucuggcacggugaagagacaugagagacucugaucguuu
uuucacugacccggugaggcgggggggcgagccccgaggggcucucgcuu
cuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggg
gacagugccagguggggaguuugacuggggcgguacaccugucaaacggu
aacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugga
gcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagac
cgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcagg
aggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcg
uucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucau
ugugaagcagaauucaccaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacuga
ugauguguuguugccaugguaauccugcucaguacgagaggaaccgcagg
uucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcu
accaucugugggauuaugacugaacgccucuaagucagaaucccgcccag
gcggaacgauacggcagcgccgcggagccucgguuggccucggauagccg
gucccccgccgggguccggugcggagugcccuucguccugggaaacgggg
cgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu
.........................<<<<<<.....<<....>>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<.<<<.....<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>.>>>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
....<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<..<.
....<<<<.<<<..<<<<..>>>>>>>>>>>.>..>>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
<<<<<...<<..<<<....<<<<......<<<<<<<<..>>>>>>>>...
....>>>>...>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<<<<<<<<<<<<<.<<<<....>>>>.>>>>>>
.>>>>.>>>>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<..
...>>>>>>>>.>>....>>>>>>......>>.>>>>>....>>>>...>
>>>>>>>..<<<<........>>>><<<<<<...<<<<<<<<<<<<<<..
<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<<
<......>>>>>>>..<<<<<...<<<..<<<..((((.((((>>>..>>
>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>
>>>>>>>>>>>>>.<<.<..<<<<<<<.....<<<<<<<<<..<<<....
<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>
>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..
>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<..........
..........<<<.<<<<<<<<<...<<<....<<<..<.<<<..<<<<.
............>>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<
<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<
<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<
<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<...
....<<<<<.<<<...<<.........>>...>>>.........<<....
..>>...>>>>>...>>>>>>>>>>>>>..........))).>>...>>>
>>..>>>...>>>>>>><<<<<<.<<<..........)))).))))...<
.....>..................>>>>>>>>>....>>>>>>...<<<<
<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>...
.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<..
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<
<...<<....<<<....>>>..........<<.<<<<<...<....>..>
>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<...
.<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<
<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<
<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>...
..<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>........
.>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.
<<.........<.....<<<<<...............>>>>><<.<<<<<
<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>.....
.......<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<
.....>>>>......>>>>>>>...<<..<<<..<<<<<<.....<<...
..<<<<....>>>>.....>>..>>>>..>>>>><<<<<<.......>>>
>>>........<...........<<<<<.......>>>>>.....>....
.>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....
<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<<<
<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<<.<....>.>.>>.>>>>
>>>>>>...<<<<<.....<<<<.....<..............>......
..........<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>
....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<........
...>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....
<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>><
<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>>>
>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<<.
......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<
.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>.
.>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>
>.....<<<<<<.<..<<<..<.<<<<<.................>>>>>
.><<<<....<<<<...<<<.<<<<<<<]]].>>>>>..>>.>>>..>>>
>...>>>><<<<....<<<<<...........>>>>>....>>>>.>>>.
..>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<
<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<<
.<<<<<<<......>>>>>>>>>>>...>>>>..>>>.............
.>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<<<<
<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>....
>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8yoo Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R77 I79 N88 E89 R92 T93 K170
Binding residue
(residue number reindexed from 1)		R76 I78 N87 E88 R91 T92 K169
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
PDBsum8yoo
PubMed38942792
UniProtP62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)

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