Structure of PDB 8y0w Chain Lk Binding Site BS01

Receptor Information

>8y0w Chain Lk (length=69) Species: 9606 (Homo sapiens)

PRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKE
KAEKLKQSLPPGLAVKELK

Ligand information

>8y0w Chain L5 (length=3666)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagugaucguuuuuuc
acugacccggugaggcgggggggcgagccccgaggggcucucgcuucugg
cgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggaca
gugccagguggggaguuugacuggggcgguacaccugucaaacgguaacg
cagguguccuaaggcgagcucagggaggacagaaaccucccguggagcag
aagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgug
aaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggu
gucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuca
uagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucaccaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugau
guguuguugccaugguaauccugcucaguacgagaggaaccgcagguuca
gacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacca
ucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgg
aacgauacggcagcgccgcggagccucgguuggccucggauagccggucc
cccgccgggguccggugcggagugcccuucguccugggaaacggggcgcg
gccggagaggcggccgcccccucgcccgucacgcaccgcacguucguggg
gaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuu
cguacguagcagagcagcucccucgcugcgaucuauugaaagucagcccu
cgacacaaggguuugu

.........................<<<<<<.....<......>......
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>>>>>>..[[[..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<.<
....<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<<..<.
....<<<<.<<<..<<<....>>>>>>>>>>.>..>>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
<<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>>>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<..............>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<.<<<<..<<<<..<...........>...>>>
>..>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<.
....>>>>>>>>.>>....>>>>>>.....>>>.>>>>>....>>>>...
>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<.
.<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<
<<......>>>>>>>..<<<<<...<<<..<<<..((((.{.[[>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<.........
.............<<<.<<<<<<<<<...<<<....<<<..<.<<<<.<.
.<.............>.>>>>>.>..>>>..>.>>...>>>>>>>...<<
<<<<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<
<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..
.<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<
.......<<<<<.<<....<<.........>>....>>.........<<.
.....>>...>>>>>...>>>>>>>>>>>>>..........))).>>...
>>>>>..>>>...>>>>>>><<<<<<.<<<..........]].}.)))).
..........................>>>>>>>>>....>>>>>>.<.<<
<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.
.>.....>>>>>><<<....<<.....<<<<<<.......>>>>>>.<<<
.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<
<<<...<<....<<<....>>>..........<<.<<<<<.<.<...>.>
.>>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<.
...<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<
<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{{..>>>>>>....<<
<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.
....<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>......
...>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<.
.....>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<
<.<<.........<.....<<<<<....<<..>>.....>>>>><<.<<<
<<<<<<<<...<..........>........>>>>>..>>>>>>.>>...
.........<<<<<<<<<..<<<.........>>>..<<<<<<<....<<
<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....<<<.
....<<<<....>>>>.....>>>.>>>>..>>>>><<<<<<.......>
>>>>>........<...........<<<<<.......>>>>>.....>..
...>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>>>..
..<<<<<........>>>>>....[[[[[..{{{.{{......[[[[.{{
[[[[..<<<<<.<<<<<<<<<.<<<<<<<<..............>>>>>>
>>...<<<<<.....<<<<...............................
......<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>....
>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>
>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[
.(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<.
...>>>.>>)))]......((((((..(((..>>>>>>.)))))))))..
........]]]]..}}]]]].......<<.<.<.<<<<<<...<<.....
..>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<<
<<......>>>>>...>.>.<<<.........>>>.....>>>>>..>..
.>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]...
..<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<
<<....<<<<....<<.<<<<<<<}}}.>>>>>..>>.>>...>>>>...
>>>><<<<....<<<<<...........>>>>>....>>>>.>>>...>.
>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<<.<<
<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<
<<<<......>>>>>>>>>>>...>>>>..>>>..............>>>
>..>>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<
.....<<<<.<..<<<<<......>>>>>..>>>>>....>>....>>>>
.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): P2 R3 D19 K24 K26 K33 K35 R37 S39 R40 Y41 L42 T44 L69
• Binding residue (residue number reindexed from 1): P1 R2 D18 K23 K25 K32 K34 R36 S38 R39 Y40 L41 T43 L68

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001501 skeletal system development
• GO:0001503 ossification
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0007605 sensory perception of sound
• GO:0022618 protein-RNA complex assembly
• GO:0034463 90S preribosome assembly
• GO:0042474 middle ear morphogenesis
• GO:0048318 axial mesoderm development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0033291 eukaryotic 80S initiation complex
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
• PDBsum: 8y0w
• PubMed: 38698775
• UniProt: P63173|RL38_HUMAN Large ribosomal subunit protein eL38 (Gene Name=RPL38)