Structure of PDB 8yop Chain Lo Binding Site BS01

Receptor Information

>8yop Chain Lo (length=105) Species: 9606 (Homo sapiens)

VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQF

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

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

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): V2 N3 P5 R8 R9 T10 F11 K13 G16 K17 H18 Y26 K28 G29 D31 S32 Y34 A35 Q36 G37 R39 R40 R43 K44 G47 Y48 G50 Q51 T52 K53 P54 I55 F56 R57 A60 K61 T63 K64 K65 V67 K80 R81 M82 K86 C88 K89 K97 K98
• Binding residue (residue number reindexed from 1): V1 N2 P4 R7 R8 T9 F10 K12 G15 K16 H17 Y25 K27 G28 D30 S31 Y33 A34 Q35 G36 R38 R39 R42 K43 G46 Y47 G49 Q50 T51 K52 P53 I54 F55 R56 A59 K60 T62 K63 K64 V66 K79 R80 M81 K85 C87 K88 K96 K97

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yop, PDBe:8yop, PDBj:8yop
• PDBsum: 8yop
• PubMed: 38942792
• UniProt: P83881|RL36A_HUMAN Large ribosomal subunit protein eL42 (Gene Name=RPL36A)