Structure of PDB 8y0w Chain SC Binding Site BS01

Receptor Information
>8y0w Chain SC (length=218) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLK
IMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAP
VPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKE
TVFTKSPYQEFTDHLVKT
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)		V112 Q113 K114 Q115 T116 R117 A118 R121 R123 K125 K145 K183 T185 R187 G189 S190 R194 V205 S206 A207 Y223 T224 A226 R227 C229 T230 T232 N235 K238 Y250
Binding residue
(residue number reindexed from 1)		V54 Q55 K56 Q57 T58 R59 A60 R63 R65 K67 K87 K125 T127 R129 G131 S132 R136 V147 S148 A149 Y165 T166 A168 R169 C171 T172 T174 N177 K180 Y192
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0017134 fibroblast growth factor binding
GO:0019899 enzyme binding
GO:0045296 cadherin binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0051443 positive regulation of ubiquitin-protein transferase activity
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005925 focal adhesion
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
PDBsum8y0w
PubMed38698775
UniProtP15880|RS2_HUMAN Small ribosomal subunit protein uS5 (Gene Name=RPS2)

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