Structure of PDB 8yoo Chain Sf Binding Site BS01

Receptor Information

>8yoo Chain Sf (length=67) Species: 9606 (Homo sapiens)

YTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMAS
HFDRHYCGKCCLTYCFN

Ligand information

>8yoo Chain S2 (length=1719)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuuggcucucggcgcccgaagcauu
uacuuugaaaaaauuagaguguucaaagcaggcccgagccgccuggauac
cgcagcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuuc
ggaacugaggccaugauuaagagggacggccgggggcauucguauugcgc
cgcuagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagc
auuugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaa
gacgaucagauaccgucguaguuccgaccauaaacgaugccgacuggcga
ugcggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaa
gucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaa
uugacggaagggcaccaccaggaguggagccugcggcuuaauuugacuca
acacgggaaaccucacccggcccggacacggacaggauugacagauugau
agcucuuucucgauuccgugggugguggugcauggccguucuuaguuggu
ggagcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcu
aacuaguuacgcgacccccgagcggucggcgucccccaacuucuuagagg
gacaaguggcguucagccacccgagauugagcaauaacaggucugugaug
cccuuagauguccggggcugcacgcgcgcuacacugacuggcucagcgug
ugccuacccuacgccggcaggcgcggguaacccguugaaccccauucgug
auggggaucggggauugcaauuauuccccaugaacgaggaauucccagua
agugcgggucauaagcuugcguugauuaagucccugcccuuuguacacac
cgcccgucgcuacuaccgauuggaugguuuagugaggcccucggaucggc
cccgccggggucggcccacggcccuggcggagcgcugagaagacggucga
acuugacuaucuagaggaaguaaaagucguaacaagguuuccguagguga
accugcggaaggaucauua

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

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): K89 K90 K92 H93 K94 R95 A101 Y105 V130 F131 M132 A133 S134 H135 R138 Y140 G142 K143 C145 T147
• Binding residue (residue number reindexed from 1): K5 K6 K8 H9 K10 R11 A17 Y21 V46 F47 M48 A49 S50 H51 R54 Y56 G58 K59 C61 T63

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0031386 protein tag activity
• GO:0031625 ubiquitin protein ligase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0016567 protein ubiquitination
• GO:0019941 modification-dependent protein catabolic process

Cellular Component

• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005741 mitochondrial outer membrane
• GO:0005789 endoplasmic reticulum membrane
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030666 endocytic vesicle membrane
• GO:0031982 vesicle
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8yoo, PDBe:8yoo, PDBj:8yoo
• PDBsum: 8yoo
• PubMed: 38942792
• UniProt: P62979|RS27A_HUMAN Ubiquitin-ribosomal protein eS31 fusion protein (Gene Name=RPS27A)