Structure of PDB 8yoo Chain LL Binding Site BS01

Receptor Information

>8yoo Chain LL (length=207) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDVE

Ligand information

>8yoo Chain L5 (length=3670)

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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>>.>>>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
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................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
....<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<..<.
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>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
<<<<<...<<..<<<....<<<<......<<<<<<<<..>>>>>>>>...
....>>>>...>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<<<<<<<<<<<<<.<<<<....>>>>.>>>>>>
.>>>>.>>>>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<..
...>>>>>>>>.>>....>>>>>>......>>.>>>>>....>>>>...>
>>>>>>>..<<<<........>>>><<<<<<...<<<<<<<<<<<<<<..
<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<<
<......>>>>>>>..<<<<<...<<<..<<<..((((.((((>>>..>>
>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>
>>>>>>>>>>>>>.<<.<..<<<<<<<.....<<<<<<<<<..<<<....
<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>
>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..
>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<..........
..........<<<.<<<<<<<<<...<<<....<<<..<.<<<..<<<<.
............>>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<
<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<
<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<
<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<...
....<<<<<.<<<...<<.........>>...>>>.........<<....
..>>...>>>>>...>>>>>>>>>>>>>..........))).>>...>>>
>>..>>>...>>>>>>><<<<<<.<<<..........)))).))))...<
.....>..................>>>>>>>>>....>>>>>>...<<<<
<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>...
.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<..
...<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<
<...<<....<<<....>>>..........<<.<<<<<...<....>..>
>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<...
.<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<
<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<
<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>...
..<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>........
.>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.
<<.........<.....<<<<<...............>>>>><<.<<<<<
<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>.....
.......<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<
.....>>>>......>>>>>>>...<<..<<<..<<<<<<.....<<...
..<<<<....>>>>.....>>..>>>>..>>>>><<<<<<.......>>>
>>>........<...........<<<<<.......>>>>>.....>....
.>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....
<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<<<
<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<<.<....>.>.>>.>>>>
>>>>>>...<<<<<.....<<<<.....<..............>......
..........<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>
....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<........
...>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....
<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>><
<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>>>
>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<<.
......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<
.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>.
.>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>
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.><<<<....<<<<...<<<.<<<<<<<]]].>>>>>..>>.>>>..>>>
>...>>>><<<<....<<<<<...........>>>>>....>>>>.>>>.
..>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<
<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<<
.<<<<<<<......>>>>>>>>>>>...>>>>..>>>.............
.>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<<<<
<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>....
>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yoo Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): A2 S4 R5 M8 L10 K11 P12 H13 F14 H15 K16 W18 Q19 R20 W25 Q28 P29 R31 K32 R35 R36 R39 K42 R44 R45 R56 V59 R60 C61 P62 T63 Y66 H67 R71 G73 R74 L78 R92 D99 P100 R101 R102 R103 S106 R129 K130 K135 R158 K163 K165 F179 R183 M184 R186 A187 N188 L191 G193 R195 K197 R198
• Binding residue (residue number reindexed from 1): A1 S3 R4 M7 L9 K10 P11 H12 F13 H14 K15 W17 Q18 R19 W24 Q27 P28 R30 K31 R34 R35 R38 K41 R43 R44 R55 V58 R59 C60 P61 T62 Y65 H66 R70 G72 R73 L77 R91 D98 P99 R100 R101 R102 S105 R128 K129 K134 R157 K162 K164 F178 R182 M183 R185 A186 N187 L190 G192 R194 K196 R197

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• 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

External links

• PDB: RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
• PDBsum: 8yoo
• PubMed: 38942792
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)