Structure of PDB 8ink Chain Y Binding Site BS02

Receptor Information

>8ink Chain Y (length=167) Species: 9606 (Homo sapiens)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKEQIVPKPEEEVAQKK

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): V2 R3 Y4 L6 R18 S20 H25 K27 R30 Q34 K37 K43 K55 R62 Y63 N64 G65 G66 G68 R69 A71 Q72 K74 Q75 Q80 R82 W83 K86 N97 S100 N101 L104 Q118 V119 R127 Y130 R131 A132 H133 I136 N137 P138 Y139 M140 S141
• Binding residue (residue number reindexed from 1): V1 R2 Y3 L5 R17 S19 H24 K26 R29 Q33 K36 K42 K54 R61 Y62 N63 G64 G65 G67 R68 A70 Q71 K73 Q74 Q79 R81 W82 K85 N96 S99 N100 L103 Q117 V118 R126 Y129 R130 A131 H132 I135 N136 P137 Y138 M139 S140

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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ink, PDBe:8ink, PDBj:8ink
• PDBsum: 8ink
• PubMed: 37491604
• UniProt: P18621|RL17_HUMAN Large ribosomal subunit protein uL22 (Gene Name=RPL17)