Structure of PDB 8k2c Chain LX Binding Site BS01

Receptor Information
>8k2c Chain LX (length=120) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESA
MKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKA
YVRLAPDYDALDVANKIGII
Ligand information
>8k2c 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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PDB8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
P44 T45 F46 R47 R48 P49 K50 T51 R53 L54 R56 Q57 K59 Y60 R62 T83 S85 K89 N93 N105 K106 H107 K123 N125 T126 L127 I128 P130 K134 K135 Y137 R139
Binding residue
(residue number reindexed from 1)
P8 T9 F10 R11 R12 P13 K14 T15 R17 L18 R20 Q21 K23 Y24 R26 T47 S49 K53 N57 N69 K70 H71 K87 N89 T90 L91 I92 P94 K98 K99 Y101 R103
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0045296 cadherin binding
GO:1904841 TORC2 complex binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
PDBsum8k2c
PubMed38942792
UniProtP62750|RL23A_HUMAN Large ribosomal subunit protein uL23 (Gene Name=RPL23A)

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