Structure of PDB 8ink Chain j Binding Site BS01

Receptor Information

>8ink Chain j (length=111) Species: 9606 (Homo sapiens)

RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVR
IDTRLNKAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTT
FKNLQTVNVDE

Ligand information

>8ink Chain 2 (length=3495)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaacacggaccaaggagucuaacacgugcgcga
gucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgg
cgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgagg
gcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcu
ggcguggagccgggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagacccagaaaagguguugguugauauagacagcag
gacgguggccauggaagucggaauccgcuaaggaguguguaacaacucac
cugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggccc
auacccggccgucgccggcagucgagaguggacgggagcggcggcccgga
gccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagcc
uugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuu
ggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggaga
aggguuccaugugaacagcaguugaacaugggucagucgguccugagaga
ugggcgagcgccguuccgaagggacgggcgauggccuccguugcccucgg
ccgaucgaaagggagucggguucagauccccgaauccggaguggcggaga
ugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagc
cggcgggagccccggggagaguucucuuuucuuugugaagggcagggcgc
ccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgucg
cgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgggg
gagaggguguaaaucucgcgccgggccguacccauauccgcagcaggucu
ccaaggugaacagccucuggcauguuggaacaauguagguaagggaaguc
ggcaagccggauccguaacuucgggauaaggauuggcucuaagggcuggg
ucggucgcggccggcgccuagcagccgacuuagaacuggugcggaccagg
ggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggg
uguugacgcgaugugauuucugcccagugcucugaaugucaaagugaaga
aauucaaugaagcgcggguaaacggcgggaguacucucuuaagaacgaga
uucccacugucccuaccuacuauccagcgaaaccacagccaagggaacgg
gcuuggcggaaucagcggggaaagaagacccuguugagcuugacucuagu
cuggcacggugaaguuuuuucacugacccggugaggcgggggggcgagcc
ccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuuccugucgcagg
uguccuaaggcgagcucagggaggacagaaaccucccguggagcagaagg
gcaaaagcucgcuugaucuugauuuuuacgaauacagaccgugaaagcgg
ggccgauccuucugaccuuuuggguuuuaagcaggagguaaguuaccaca
gggauaggcuuguggcggccaagcguucauagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauacggcagcgccgcgg
agccucgguuggccucggauagccggucccccgccgggguccggugcgga
gugcccuucguccugggaaacggggcgcggccggagaggcggccgccccc
ucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauuc
guagacgaccugcuucugggucgggguuucguacguagcagagcagcucc
cucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ink Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R23 T26 H30 K31 R32 H34 G35 F38 K39 R41 K47 R50 K55 I64 N69 K70 W73 K75 I77 R78 N79 Y82 R83 N116 L117 Q118 T119
• Binding residue (residue number reindexed from 1): R10 T13 H17 K18 R19 H21 G22 F25 K26 R28 K34 R37 K42 I51 N56 K57 W60 K62 I64 R65 N66 Y69 R70 N103 L104 Q105 T106

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ink, PDBe:8ink, PDBj:8ink
• PDBsum: 8ink
• PubMed: 37491604
• UniProt: P62899|RL31_HUMAN Large ribosomal subunit protein eL31 (Gene Name=RPL31)