Structure of PDB 8yop Chain LA Binding Site BS01

Receptor Information

>8yop Chain LA (length=248) Species: 9606 (Homo sapiens)

GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHD
PGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNV
LPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLP
SGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRG
VAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGT

Ligand information

>8yop Chain L5 (length=3771)

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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): G2 R3 V4 R6 G7 Q8 R9 K10 G11 A12 S14 V15 R17 A18 H19 V20 K21 H22 R23 K24 G25 A26 F34 R37 H38 G39 Y40 I44 H50 P52 R54 R64 Y67 R68 F69 K70 K71 R72 T84 G85 F87 Y89 A94 Q95 E118 G121 D122 K125 L126 A127 R128 A129 S130 G131 N132 L150 P151 S152 S154 K156 G172 R174 I175 K177 P178 I179 L180 K181 A182 G183 H187 K188 K190 K192 R193 N194 W196 R198 V199 R200 G201 V202 A203 M204 N205 P206 V207 E208 H209 F211 G213 G214 N215 H216 Q217 H218 G220 K221 P222 S223 T224 I225 R226 R227 D228 P230 A231 G232 R233 K234 V235 G236 L237 I238 A239 A240 R241 R242 T243 G244 R245
• Binding residue (residue number reindexed from 1): G1 R2 V3 R5 G6 Q7 R8 K9 G10 A11 S13 V14 R16 A17 H18 V19 K20 H21 R22 K23 G24 A25 F33 R36 H37 G38 Y39 I43 H49 P51 R53 R63 Y66 R67 F68 K69 K70 R71 T83 G84 F86 Y88 A93 Q94 E117 G120 D121 K124 L125 A126 R127 A128 S129 G130 N131 L149 P150 S151 S153 K155 G171 R173 I174 K176 P177 I178 L179 K180 A181 G182 H186 K187 K189 K191 R192 N193 W195 R197 V198 R199 G200 V201 A202 M203 N204 P205 V206 E207 H208 F210 G212 G213 N214 H215 Q216 H217 G219 K220 P221 S222 T223 I224 R225 R226 D227 P229 A230 G231 R232 K233 V234 G235 L236 I237 A238 A239 R240 R241 T242 G243 R244

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0098794 postsynapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yop, PDBe:8yop, PDBj:8yop
• PDBsum: 8yop
• PubMed: 38942792
• UniProt: P62917|RL8_HUMAN Large ribosomal subunit protein uL2 (Gene Name=RPL8)