Structure of PDB 8y0x Chain Lp Binding Site BS01

Receptor Information

>8y0x Chain Lp (length=91) Species: 9606 (Homo sapiens)

AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRA
VGIWHCGSCMKTVAGGAWTYNTTSAVTVKSAIRRLKELKDQ

Ligand information

>8y0x Chain L5 (length=3658)

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
ccgcggcggguguugacgcgaugugauuucugcccagugcucucaaagug
aagaaauucaaugaagcgcggguaaacggcgggaguaacuaugucucuua
agguagccaaaugccucgucaucuaauuagugacgcgcaugaauggauga
acgagauucccacugucccuaccuacuauccagcgaaaccacagccaagg
gaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugac
ucuagucuggcacggugaagagacaugagugaucguuuuuucacugaccc
ggugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagc
gcccggccgcgcgccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauac
ggcagcgccgcggagccucgguuggccucggauagccggucccccgccgg
gguccggugcggagugcccuucguccugggaaacggggcgcggccggaga
ggcggccgcccccucgcccgucacgcaccgcacguucguggggaaccugg
cgcuaaaccauucguagacgaccugcuucugggucgggguuucguacgua
gcagagcagcucccucgcugcgaucuauugaaagucagcccucgacacaa
ggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0x The global structure of dormant ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): A2 R4 T5 K6 V8 G9 I10 G12 K13 Y14 T16 R17 Y18 G19 A20 S21 R23 H34 C42 K46 A51 G58 S59 W69
• Binding residue (residue number reindexed from 1): A1 R3 T4 K5 V7 G8 I9 G11 K12 Y13 T15 R16 Y17 G18 A19 S20 R22 H33 C41 K45 A50 G57 S58 W68

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0x, PDBe:8y0x, PDBj:8y0x
• PDBsum: 8y0x
• PubMed: 38698775
• UniProt: P61513|RL37A_HUMAN Large ribosomal subunit protein eL43 (Gene Name=RPL37A)