Structure of PDB 8yoo Chain Lj Binding Site BS01

Receptor Information
>8yoo Chain Lj (length=86) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSA
KAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKPK
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)
T2 K3 G4 T5 S6 S7 F8 G9 K10 R11 R12 N13 K14 T15 H16 K25 H28 Q30 G35 K36 R43 K44 R45 K46 Y47 N48 W49 K52 R55 R56 T58 T59 Y71 R75
Binding residue
(residue number reindexed from 1)
T1 K2 G3 T4 S5 S6 F7 G8 K9 R10 R11 N12 K13 T14 H15 K24 H27 Q29 G34 K35 R42 K43 R44 K45 Y46 N47 W48 K51 R54 R55 T57 T58 Y70 R74
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
GO:0046872 metal ion binding
GO:0097371 MDM2/MDM4 family protein binding
GO:1990948 ubiquitin ligase inhibitor activity
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:1901798 positive regulation of signal transduction by p53 class mediator
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
GO:1990904 ribonucleoprotein complex

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Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
PDBsum8yoo
PubMed38942792
UniProtP61927|RL37_HUMAN Large ribosomal subunit protein eL37 (Gene Name=RPL37)

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