Structure of PDB 8y0w Chain SD Binding Site BS01

Receptor Information
>8y0w Chain SD (length=227) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIII
LATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIA
QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSM
KFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGP
KKPLPDHVSIVEPKDEILPTTPISEQK
Ligand information
>8y0w Chain S2 (length=1735) [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
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcguuuacuuugaaaaaauuagaguguucaaagc
aggcccgccuggauaccgcagcuaggaauaauggaauaggaccgcgguuc
uauuuuguugguuuucggaacugaggccaugauuaagagggacggccggg
ggcauucguauugcgccgcuagaggugaaauucuuggaccggcgcaagac
ggaccagagcgaaagcauuugccaagaauguuuucauuaaucaagaacga
aagucggagguucgaagacgaucagauaccgucguaguuccgaccauaaa
cgaugccgaccggcgaugcggcggcguuauucccaugacccgccgggcag
cuuccgggaaaccaaagucuuuggguuccggggggaguaugguugcaaag
cugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccugc
ggcuuaauuugacucaacacgggaaaccucacccggcccggacacggaca
ggauugacagauugauagcucuuucucgauuccgugggugguggugcaug
gccguucuuaguugguggagcgauuugucugguuaauuccgauaacgaac
gagacucuggcaugcuaacuaguuacgcgacccccgagcggucggcgucc
cccaacuucuuagagggacaaguggcguucagccacccgagauugagcaa
uaacaggucugugaugcccuuagauguccggggcugcacgcgcgcuacac
ugacuggcucagcgugugccuacccuacgccggcaggcgcggguaacccg
uugaaccccauucgugauggggaucggggauugcaauuauuccccaugaa
cgaggaauucccaguaagugcgggucauaagcuugcguugauuaaguccc
ugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguuuagug
aggcccucggaucggccccgccggggucggcccacggcccuggcggagcg
cugagaagacggucgaacuugacuaucuagaggaaguaaaagucguaaca
agguuuccguaggugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.<<<.....>>>.>>......>>.........<<<<...<<<<.....
...>>>>...>>>><<..<<<<<...<......>..>>>>>......>>.
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<<..>>>.>...>>>>>>.........<<<....<<<.....>>>..>>>
..>...>>.>.....<<.....<<..<<....>>..>>.......>>...
...<<..<...........>..>>.........<<<<<((....<.<<<<
.....<<..))>>.......>>>>>>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<.......................<<.
<.............>>>...<<<<<<.<.......<<...<.......>.
<<<<..>>>>...>>......>.>>>..>>>........<.<<.<<<.<<
<...............>>>.>>>.>>.>....>>....<<<<<<..<...
<<<<..<<..<<<<<<<<...<<<......>>>......>>>>>>>>..>
>.......<<....>>...>>>>..>..>>>.>>>...>>>...>>.>..
..<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>......
....<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>>>.>..>
>>...<<..))>>...>>.....>>>.>.>.<<<......<<<<....>>
>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..<<<.<<<
<<<......<<........>>..........<<<<<......<<<<<<..
.....<<.<<<........>>>.>>.....>>>>>>...<<.<<<..<<.
<<<<<<....<<<.<<<<<....>>>...<<<......>>>...>>.>>>
....<<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>>>>..
...>>>>..>>>>..>.....<<<<<.....>>>>>........>>>...
.>>>.>>>.....>>>>>>>.......>>>>>...>>.>>>>.>>>....
.<<.<<<........<.......<<<.<<<<....>>>>.>>>....>..
.......>>>.>>......<...<.<<<<<..........>>>>>>....
>.....>>>>>.....<<<<<<<<.......>>>>>>>>......>>...
>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<.<<<<<<.<<<.
.<<<<.<<...<<<<<...<<.....................>>.....>
>>>>...>>.>>>>..>>>.>>>>>>.>...>>.>>>>...>.>>...>.
....<<<<<<<<<<..>>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
Resolution3.4 Å
Binding residue
(original residue number in PDB)		Q4 I5 S6 K7 K8 R9 A114 S139 G140 K141 Q145 R146 K151 I158 H159 S160 G161 D162 P163 V172 H174 R178 Q179 G180 V181 K185 D206
Binding residue
(residue number reindexed from 1)		Q4 I5 S6 K7 K8 R9 A114 S139 G140 K141 Q145 R146 K151 I158 H159 S160 G161 D162 P163 V172 H174 R178 Q179 G180 V181 K185 D206
Enzymatic activity
Enzyme Commision number 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0004520 DNA endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0015631 tubulin binding
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0019899 enzyme binding
GO:0019900 kinase binding
GO:0019901 protein kinase binding
GO:0030544 Hsp70 protein binding
GO:0032357 oxidized purine DNA binding
GO:0032358 oxidized pyrimidine DNA binding
GO:0044390 ubiquitin-like protein conjugating enzyme binding
GO:0044877 protein-containing complex binding
GO:0051018 protein kinase A binding
GO:0051536 iron-sulfur cluster binding
GO:0051879 Hsp90 protein binding
GO:0070181 small ribosomal subunit rRNA binding
GO:0097100 supercoiled DNA binding
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0140297 DNA-binding transcription factor binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006412 translation
GO:0006413 translational initiation
GO:0006417 regulation of translation
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007059 chromosome segregation
GO:0010628 positive regulation of gene expression
GO:0017148 negative regulation of translation
GO:0031116 positive regulation of microtubule polymerization
GO:0031334 positive regulation of protein-containing complex assembly
GO:0031397 negative regulation of protein ubiquitination
GO:0032079 positive regulation of endodeoxyribonuclease activity
GO:0032743 positive regulation of interleukin-2 production
GO:0034614 cellular response to reactive oxygen species
GO:0042104 positive regulation of activated T cell proliferation
GO:0042981 regulation of apoptotic process
GO:0043507 positive regulation of JUN kinase activity
GO:0045738 negative regulation of DNA repair
GO:0045739 positive regulation of DNA repair
GO:0050862 positive regulation of T cell receptor signaling pathway
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0051225 spindle assembly
GO:0051301 cell division
GO:0061481 response to TNF agonist
GO:0070301 cellular response to hydrogen peroxide
GO:0071356 cellular response to tumor necrosis factor
GO:1901224 positive regulation of non-canonical NF-kappaB signal transduction
GO:1902231 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1905053 positive regulation of base-excision repair
GO:2001235 positive regulation of apoptotic signaling pathway
GO:2001272 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005783 endoplasmic reticulum
GO:0005819 spindle
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0014069 postsynaptic density
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032587 ruffle membrane
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0071159 NF-kappaB complex
GO:0072686 mitotic spindle
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
PDBsum8y0w
PubMed38698775
UniProtP23396|RS3_HUMAN Small ribosomal subunit protein uS3 (Gene Name=RPS3)

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