Structure of PDB 8y0x Chain LU Binding Site BS01

Receptor Information

>8y0x Chain LU (length=101) Species: 9606 (Homo sapiens)

QVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERS
KSKITVTSEVPFSKRYLKYLTKKYLKKNNLRDWLRVVANSKESYELRYFQ
I

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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<...<<<<<...........>>>>>...>>>>>.>>>...>.>>>>>>..
...<<<<<<<.<<..<<<<....<<<........<<<<<.<<<<....>>
>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<<....
..>>>>>>>>>>>...>>>>..>>>..............>>>>..>>>>>
>>>><<<<<.<.............>....<<.<<<<<<<.<<.....<<<
<.<..<<<<<......>>>>>..>>>>>....>>....>>>>.>>>.>>.
.>>>>>..

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): K48 N50 G51 S79 K80 R81 Y82 K84 Y85 K89 K92 R97 R101 A104 K107 Y110 R113
• Binding residue (residue number reindexed from 1): K32 N34 G35 S63 K64 R65 Y66 K68 Y69 K73 K76 R81 R85 A88 K91 Y94 R97

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008201 heparin binding
• GO:0042802 identical protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046632 alpha-beta T cell differentiation
• GO:0140236 translation at presynapse

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:0045202 synapse
• GO:0070062 extracellular exosome
• GO:0098793 presynapse
• GO:0098978 glutamatergic synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0x, PDBe:8y0x, PDBj:8y0x
• PDBsum: 8y0x
• PubMed: 38698775
• UniProt: P35268|RL22_HUMAN Large ribosomal subunit protein eL22 (Gene Name=RPL22)