Structure of PDB 8y0w Chain S Binding Site BS01

Receptor Information
>8y0w Chain S (length=55) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DGFDSRGKREFDRHSGSDRSGLKHEDKRGGSGSHNWGTVKDELTLDEWKA
IQNKD
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)		R188 K190 R191 F193 D194 R195 H196 S197 G198 R201 G203 L204 K205 K209 R210 S213 G214 S215 H216
Binding residue
(residue number reindexed from 1)		R6 K8 R9 F11 D12 R13 H14 S15 G16 R19 G21 L22 K23 K27 R28 S31 G32 S33 H34
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0030371 translation repressor activity
GO:0032183 SUMO binding
GO:0043022 ribosome binding
GO:0045296 cadherin binding
GO:0061770 translation elongation factor binding
Biological Process
GO:0006417 regulation of translation
GO:0017148 negative regulation of translation
GO:0030578 PML body organization
GO:0043488 regulation of mRNA stability
GO:0141014 ribosome hibernation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

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
UniProtQ8NC51|SERB1_HUMAN SERPINE1 mRNA-binding protein 1 (Gene Name=SERBP1)

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