Structure of PDB 8ipy Chain S Binding Site BS01

Receptor Information

>8ipy Chain S (length=135) Species: 9606 (Homo sapiens)

VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMP
FKCMQLTDFILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERK
AKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALL

Ligand information

>8ipy Chain 2 (length=3485)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcagacccga
cgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcugg
cguggagccgggcguggaaugcgagugccuagugggccacuuuugguaag
cagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaug
ccgacgcucaucagacccagaaaagguguugguugauauagacagcagga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccu
gccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccau
acccggccgucgccggcagucgagaguggacgggagcggcggcccggagc
cccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuu
gaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuugg
ugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaag
gguuccaugugaacagcaguugaacaugggucagucgguccugagagaug
ggcgagcgccguuccgaagggacgggcgauggccugcccuccgaucgaaa
gggagucggguucagauccccgaauccggaguggcggagaugggcgccgc
gaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggagc
cccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaugg
guucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggc
ggcguccggugagcucucgcuggcccuugaaaauccgggggagagggugu
aaaucucgcgccgggccguacccauauccgcagcaggucuccaaggugaa
cagccucuggcauguuggaacaauguagguaagggaagucggcaagccgg
auccguaacuucgggauaaggauuggcucuaagggcugggucggucgcgg
ccggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgggaguacucucuuaagaacgagauucccacugu
cccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggcgga
aucagcggggaaagaagacccuguugagcuugacucuagucuggcacggu
gaaguuuuuucacugacccggugaggcgggggggcgagccccgaggggcu
cucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccg
cuccggggacagugccagguggggaguuuccugucgcagguguccuaagg
cgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcuc
gcuugaucuugauuuuuacgaauacagaccgugaaagcggggccgauccu
ucugaccuuuuggguuuuaagcaggagguaaguuaccacagggauaggcu
uguggcggccaagcguucauagcgacgucgcuuuuugauccuucgauguc
ggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguuca
cccacuaauagggaacgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacugaugauguguuguugccaugguaauccugcucaguac
gagaggaaccgcagguucagacauuugguguaugugcuuggcugaggagc
caauggggcgaagcuaccaucugugggauuaugacugaacgccucuaagu
cagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgguu
ggccucggauagccggucccccgccgggguccggugcggagugcccuucg
uccugggaaacggggcgcggccggagaggcggccgcccccucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcucccucgcugcga
ucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ipy Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): F3 R5 F17 P19 H20 D29 N34 Q44 V45 R46 Q56 P65 H66 H69 Q70 K71 Y72 R74 W91 K94 R98 K101 M113 K114 K116 K117 M118 N120 I122 K128
• Binding residue (residue number reindexed from 1): F2 R4 F16 P18 H19 D28 N33 Q43 V44 R45 Q55 P64 H65 H68 Q69 K70 Y71 R73 W90 K93 R97 K100 M112 K113 K115 K116 M117 N119 I121 K127

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ipy, PDBe:8ipy, PDBj:8ipy
• PDBsum: 8ipy
• PubMed: 37491604
• UniProt: P50914|RL14_HUMAN Large ribosomal subunit protein eL14 (Gene Name=RPL14)