Structure of PDB 8yop Chain Sg Binding Site BS01

Receptor Information
>8yop Chain Sg (length=313) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETN
YGIPQRALRGHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRF
VGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCKYTVQDESHSEWV
SCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVS
PDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAA
TGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAG
YTDNLVRVWQVTI
Ligand information
>8yop Chain S2 (length=1740) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccgc
gguucuauuuuguugguuuucggaacugaggccaugauuaagagggacgg
ccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgc
aagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaag
aacgaaagucggagguucgaagacgaucagauaccgucguaguuccgacc
auaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgccg
ggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguug
caaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggag
ccugcggcuuaauuugacucaacacgggaaaccucacccggcccggacac
ggacaggauugacagauugauagcucuuucucgauuccgugggugguggu
gcauggccguucuuaguugguggagcgauuugucugguuaauuccgauaa
cgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucgg
cgucccccaacuucuuagagggacaaguggcguucagccacccgagauug
agcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgc
uacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggua
acccguugaaccccauucgugauggggaucggggauugcaauuauucccc
augaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaa
gucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguu
uagugaggcccucggaucggccccgccggggucggcccacggcccuggcg
gagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagucg
uaacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.<<<.....>>>.>>......>>.........<<<<...<<<<<....
.>.>>>>...>>>><<..<<<<<...<......>..>>>>>......>>.
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<<...>>>>..>>>
..>...>>.>.....<<<<<<<<<.<<<....>>>..>>>>>.>>>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.....<<..))>>.......>>>>.>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<.......................<<.
<<...........>>>>...<<<<<<.<.......<<...<.......>.
<<<<.......>>>>...>>......>.>>>..>>>........<.<<.<
<<<<<<...............>>>>>>>.>>.>....>>....<<<<<<.
.<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>>>
>>..>>.......<<....>>...>>>>..>..>>>.>>>...>>>...>
>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>.
.........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>>>
.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<<.
...>>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..<<
<.<<<<<<......<<........>>..........<<<<<.<....<<<
<<<.......<<.<<<........>>>.>>.....>>>>>>...<<.<<<
..<<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>...>
>.>>>....<<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>
>>>.....>>>>..>>>>..>.....<<<<<.....>>>>>........>
>>....>>>.>>>.....>>>>>>>.....>.>>>>>...>>.>>>>.>>
>.....<<.<<<........<.......<<<.<<<<....>>>>.>>>..
..>.........>>>.>>......<.....<<<<<..........>>>>>
.....>.....>>>>>.....<<<<<<<<.......>>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<
.<<<..<<<<.<<...<<<<<...<<<...................>>>.
....>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.>>
...>.....<<<<<<<<<<..>>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8yop Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N15 G61 S63 H64 R88 R100 K280 A281
Binding residue
(residue number reindexed from 1)		N14 G60 S62 H63 R87 R99 K279 A280
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005080 protein kinase C binding
GO:0005102 signaling receptor binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0008200 ion channel inhibitor activity
GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0019899 enzyme binding
GO:0019903 protein phosphatase binding
GO:0030292 protein tyrosine kinase inhibitor activity
GO:0030332 cyclin binding
GO:0030971 receptor tyrosine kinase binding
GO:0035591 signaling adaptor activity
GO:0042169 SH2 domain binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043022 ribosome binding
GO:0045296 cadherin binding
GO:0051434 BH3 domain binding
GO:0060090 molecular adaptor activity
Biological Process
GO:0001934 positive regulation of protein phosphorylation
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0006417 regulation of translation
GO:0006915 apoptotic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007369 gastrulation
GO:0010629 negative regulation of gene expression
GO:0016567 protein ubiquitination
GO:0017148 negative regulation of translation
GO:0030178 negative regulation of Wnt signaling pathway
GO:0030308 negative regulation of cell growth
GO:0030335 positive regulation of cell migration
GO:0031334 positive regulation of protein-containing complex assembly
GO:0032091 negative regulation of protein binding
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032880 regulation of protein localization
GO:0033137 negative regulation of peptidyl-serine phosphorylation
GO:0042998 positive regulation of Golgi to plasma membrane protein transport
GO:0043065 positive regulation of apoptotic process
GO:0043473 pigmentation
GO:0043547 positive regulation of GTPase activity
GO:0045879 negative regulation of smoothened signaling pathway
GO:0048511 rhythmic process
GO:0050765 negative regulation of phagocytosis
GO:0051302 regulation of cell division
GO:0051726 regulation of cell cycle
GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051901 positive regulation of mitochondrial depolarization
GO:0071333 cellular response to glucose stimulus
GO:0071363 cellular response to growth factor stimulus
GO:0072344 rescue of stalled ribosome
GO:0106070 regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway
GO:1900102 negative regulation of endoplasmic reticulum unfolded protein response
GO:1903751 negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide
GO:2000114 regulation of establishment of cell polarity
GO:2000543 positive regulation of gastrulation
GO:2001244 positive regulation of intrinsic apoptotic signaling pathway
Cellular Component
GO:0001891 phagocytic cup
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005886 plasma membrane
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:0030425 dendrite
GO:0030496 midbody
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043204 perikaryon
GO:0044297 cell body
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:1990630 IRE1-RACK1-PP2A complex
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8yop, PDBe:8yop, PDBj:8yop
PDBsum8yop
PubMed38942792
UniProtP63244|RACK1_HUMAN Small ribosomal subunit protein RACK1 (Gene Name=RACK1)

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