Structure of PDB 8k2c Chain LE Binding Site BS01

Receptor Information

>8k2c Chain LE (length=221) Species: 9606 (Homo sapiens)

PHCSRNPVLVRGIGRYSRSAMYSRKAMYKRKYSAAVLATVTKPVGGDKNG
GTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILII
LTGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKID
ISNVKIPKHLTDAYFKKKKKEKYEITEQRKIDQKAVDSQILPKIKAIPQL
QGYLRSVFALTNGIYPHKLVF

Ligand information

>8k2c 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: 8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): H43 C44 S45 R46 V51 R52 S58 R59 S60 M62 Y63 R65 K66 A67 Y69 K70 R71 K72 Y73 V88 L89 A90 T91 K94 P95 G97 D99 K100 N101 R105 V107 K108 R110 K111 M112 P113 R114 Y115 V121 R123 K124 L125 L126 S127 H128 G129 K130 P132 F133 S134 H136 K139 T154 R156 H157 R158 L172 L179 L181 R183 P185 R187 R188 H190 K192 F193 F217 K218 K219 Y240 I242 K262 Q266 Q268 R272 S273 N279
• Binding residue (residue number reindexed from 1): H2 C3 S4 R5 V10 R11 S17 R18 S19 M21 Y22 R24 K25 A26 Y28 K29 R30 K31 Y32 V36 L37 A38 T39 K42 P43 G45 D47 K48 N49 R53 V55 K56 R58 K59 M60 P61 R62 Y63 V69 R71 K72 L73 L74 S75 H76 G77 K78 P80 F81 S82 H84 K87 T102 R104 H105 R106 L120 L127 L129 R131 P133 R135 R136 H138 K140 F141 F165 K166 K167 Y173 I175 K195 Q199 Q201 R205 S206 N212

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006355 regulation of DNA-templated transcription
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• 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:0036464 cytoplasmic ribonucleoprotein granule
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
• PDBsum: 8k2c
• PubMed: 38942792
• UniProt: Q02878|RL6_HUMAN Large ribosomal subunit protein eL6 (Gene Name=RPL6)