Structure of PDB 8yoo Chain Lo Binding Site BS01

Receptor Information

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

VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQF

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

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): V2 N3 P5 R8 R9 T10 F11 K13 G16 K17 H18 Y26 K28 G29 K30 D31 S32 Y34 A35 Q36 G37 R39 R40 R43 K44 G47 Y48 G50 Q51 K53 P54 I55 F56 R57 K58 A60 K61 T63 K64 K65 K80 R81 M82 A84 K86 R87 C88 K89 K97 K98 K100
• Binding residue (residue number reindexed from 1): V1 N2 P4 R7 R8 T9 F10 K12 G15 K16 H17 Y25 K27 G28 K29 D30 S31 Y33 A34 Q35 G36 R38 R39 R42 K43 G46 Y47 G49 Q50 K52 P53 I54 F55 R56 K57 A59 K60 T62 K63 K64 K79 R80 M81 A83 K85 R86 C87 K88 K96 K97 K99

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