Structure of PDB 8xsy Chain Li Binding Site BS01

Receptor Information
>8xsy Chain Li (length=102) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFA
PYERRAMELLKVSKDKRALKFIKKRVGTHIRAKRKREELSNVLAAMRKAA
AK
Ligand information
>8xsy Chain L5 (length=3771) [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
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcgccacgcaguuuuauccgguaaagcgaaugauuagaggucuugg
ggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagccc
ggcucgcuggcguggagccgggcguggaaugcgagugccuagugggccac
uuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaag
gcgcccgaugccgacgcucaucagaccccagaaaagguguugguugauau
agacagcaggacgguggccauggaagucggaauccgcuaaggagugugua
acaacucaccugccgaaucaacuagcccugaaaauggauggcgcuggagc
gucgggcccauacccggccgucgccggcagucgagaguggacgggagcgg
cggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgcug
cggugagccuugaagccuagggcgcgggcccggguggagccgccgcaggu
gcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccg
aaguggagaaggguuccaugugaacagcaguugaacaugggucagucggu
ccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccgu
ugcccucggccgaucgaaagggagucggguucagauccccgaauccggag
uggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgaucc
cggagaagccggcgggagccccggggagaguucucuuuucuuugugaagg
gcagggcgcccuggaauggguucgccccgagagaggggcccgugccuugg
aaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaa
aauccgggggagaggguguaaaucucgcgccgggccguacccauauccgc
agcaggucuccaaggugaacagccucuggcauguuggaacaauguaggua
agggaagucggcaagccggauccguaacuucgggauaaggauuggcucua
agggcugggucggucgcggccggcgccuagcagccgacuuagaacuggug
cggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcc
cgcggcggguguugacgcgaugugauuucugcccagugcucugaauguca
aagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugac
ucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaa
uggaugaacgagauucccacugucccuaccuacuauccagcgaaaccaca
gccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguuga
gcuugacucuagucuggcacggugaagagacaugagagguguagaauaag
ugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcgg
gguccgccggcccugcgggccgccggugaaauaccacuacucugaucguu
uuuucacugacccggugaggcgggggggcgagccccgaggggcucucgcu
ucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccgg
ggacagugccagguggggaguuugacuggggcgguacaccugucaaacgg
uaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugg
agcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacaga
ccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcag
gaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagc
guucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauca
uugugaagcagaauucaccaagcguuggauuguucacccacuaauaggga
acgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacug
augauguguuguugccaugguaauccugcucaguacgagaggaaccgcag
guucagacauuugguguaugugcuuggcugaggagccaauggggcgaagc
uaccaucugugggauuaugacugaacgccucuaagucagaaucccgccca
ggcggaacgauacggcagcgccgcggagccucgguuggccucggauagcc
ggucccccgccgggguccggugcggagugcccuucguccugggaaacggg
gcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguuc
guggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgg
gguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguca
gcccucgacacaaggguuugu
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<<.<<<....<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>>>>>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<..<<
....<<<<.<<<..<<<<..>>>>>>>>>>>>>..>>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
<<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>>>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<.<<<<<.<<<<<<<...........>.>>>>>
>.>>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<.
....>>>>>>>>.>>....>>>>>>......>>.>>>>>...>>>>>...
>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<.
.<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<
<<......>>>>>>>..<<<<<...<<<..<<<..((((.((((>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<.........
...........<<<.<<<<<<<<<...<<<....<<<..<.<<<....<<
.............>>..>>>.>..>>>..>.>>...>>>>>>>...<<<<
<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.
<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<
<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<..
.....<<<<<.<<<...<<.........>>...>>>.........<<...
...>>...>>>>>...>>>>>>>>>>>>>..........))).>>...>>
>>>..>>>...>>>>>>><<<<<<.<<<..........)))).))))...
<.....>..................>>>>>>>>>....>>>>>>.<.<<<
<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..
>.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<.
....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<
<<...<<....<<<....>>>..........<<.<<<<<...<....>..
>>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<..
..<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<
<<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<
<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>..
...<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>.......
..>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<..
....>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<
.<<.........<.....<<<<<....<<..>>.....>>>>><<.<<<<
<<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>....
........<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<
<.....>>>>......>>>>>>>...<<..<<<..<<<<<<.....<<..
...<<<<....>>>>.....>>..>>>>..>>>>><<<<<<.......>>
>>>>........<...........<<<<<.......>>>>>.....>...
..>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>...
.<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<<
<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<..<..............
...................<........................>.....
........................................>...>>.>>>
>>>>>>>...<<<<<.....<<<<.....<..............>.....
...........<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>
>....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<.......
....>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>....
.<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>>
<<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>>
>>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<<
.......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.
<.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>
..>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>
>>.....<<<<<<.<..<<<..<.<<<<<.................>>>>
>.><<<<....<<<<...<<<.<<<<<<<]]].>>>>>..>>.>>>..>>
>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>
...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<
<<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<
<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>............
..>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<<<
<<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>...
.>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
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PDB8xsy Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
R4 H15 V17 R25 H26 S27 R28 R29 R30 G31 R32 L33 T34 H36 R41 Y53 K65 K67 R68 R76 G78 H80 R82 K84 R85 K86
Binding residue
(residue number reindexed from 1)
R3 H14 V16 R24 H25 S26 R27 R28 R29 G30 R31 L32 T33 H35 R40 Y52 K64 K66 R67 R75 G77 H79 R81 K83 R84 K85
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0016020 membrane
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
GO:0045202 synapse
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8xsy, PDBe:8xsy, PDBj:8xsy
PDBsum8xsy
PubMed38942792
UniProtQ9Y3U8|RL36_HUMAN Large ribosomal subunit protein eL36 (Gene Name=RPL36)

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