Structure of PDB 8yoo Chain Ll Binding Site BS01

Receptor Information
>8yoo Chain Ll (length=50) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL
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
.........................<<<<<<.....<<....>>......
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>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<.<<<.....<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>.>>>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
....<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<..<.
....<<<<.<<<..<<<<..>>>>>>>>>>>.>..>>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
<<<<<...<<..<<<....<<<<......<<<<<<<<..>>>>>>>>...
....>>>>...>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<<<<<<<<<<<<<.<<<<....>>>>.>>>>>>
.>>>>.>>>>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<..
...>>>>>>>>.>>....>>>>>>......>>.>>>>>....>>>>...>
>>>>>>>..<<<<........>>>><<<<<<...<<<<<<<<<<<<<<..
<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<<
<......>>>>>>>..<<<<<...<<<..<<<..((((.((((>>>..>>
>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>
>>>>>>>>>>>>>.<<.<..<<<<<<<.....<<<<<<<<<..<<<....
<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>
>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..
>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<..........
..........<<<.<<<<<<<<<...<<<....<<<..<.<<<..<<<<.
............>>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<
<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<
<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<
<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<...
....<<<<<.<<<...<<.........>>...>>>.........<<....
..>>...>>>>>...>>>>>>>>>>>>>..........))).>>...>>>
>>..>>>...>>>>>>><<<<<<.<<<..........)))).))))...<
.....>..................>>>>>>>>>....>>>>>>...<<<<
<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>...
.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<..
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<
<...<<....<<<....>>>..........<<.<<<<<...<....>..>
>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<...
.<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<
<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<
<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>...
..<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>........
.>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.
<<.........<.....<<<<<...............>>>>><<.<<<<<
<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>.....
.......<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<
.....>>>>......>>>>>>>...<<..<<<..<<<<<<.....<<...
..<<<<....>>>>.....>>..>>>>..>>>>><<<<<<.......>>>
>>>........<...........<<<<<.......>>>>>.....>....
.>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....
<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<<<
<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<<.<....>.>.>>.>>>>
>>>>>>...<<<<<.....<<<<.....<..............>......
..........<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>
....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<........
...>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....
<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>><
<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>>>
>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<<.
......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<
.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>.
.>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>
>.....<<<<<<.<..<<<..<.<<<<<.................>>>>>
.><<<<....<<<<...<<<.<<<<<<<]]].>>>>>..>>.>>>..>>>
>...>>>><<<<....<<<<<...........>>>>>....>>>>.>>>.
..>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<
<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<<
.<<<<<<<......>>>>>>>>>>>...>>>>..>>>.............
.>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<<<<
<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>....
>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
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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)
S2 S3 H4 K5 K10 L13 Q17 I35 R36 Y37 S39 K40 R41 R42 H43 W44 R45 T47 K48 L49 L51
Binding residue
(residue number reindexed from 1)
S1 S2 H3 K4 K9 L12 Q16 I34 R35 Y36 S38 K39 R40 R41 H42 W43 R44 T46 K47 L48 L50
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0002227 innate immune response in mucosa
GO:0006412 translation
GO:0019731 antibacterial humoral response
GO:0050830 defense response to Gram-positive bacterium
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular Component
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
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
UniProtP62891|RL39_HUMAN Large ribosomal subunit protein eL39 (Gene Name=RPL39)

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