Structure of PDB 8ipx Chain r Binding Site BS01

Receptor Information
>8ipx Chain r (length=82) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKERQERKLAKDFA
RHLEEEKERRRQEKKQRRAENLKRRLENERKA
Ligand information
>8ipx Chain 2 (length=3475) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
agcgcggguaaacggcgguuaagaacgagauucccacugucccuaccuac
uauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcgggg
aaagaagacccuguugagcuugacucuagucuggcacggugaaguuuuuu
cacugacccggugaggcgggggggcgagccccgaggggcucucgcuucug
gcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggac
agugccagguggggaguuuccugucgcagguguccuaaggcgagcucagg
gaggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuu
gauuuuuacgaauacagaccgugaaagcggggccgauccuucugaccuuu
uggguuuuaagcaggagguaaguuaccacagggauaggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgcggagccucgguuggccucggau
agccggucccccgccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcac
guucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggg
ucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaa
gucagcccucgacacaaggguuugu
.........................<<<<<<.....<......>......
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..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<......>>
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<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<.......<<
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>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
.<<<<...<<..<<<..<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>.>>>........>>>>>>...>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<.<<.<<<<<<<<<<.<<<<<<.<<<<<................>>>>
>.>>>>>.>.>>>>>>>.>>>...>>.>..>>>>.>>..<<<<<<<<<..
.....>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>>...
>>>>>>>>..<<<<.....>>>><<<<<<....<<<<<<<<<<<<<..<<
<...<<<<........>>>>.....>>>...<<....>>...<<<<<<<.
.....>>>>>>>..<<<<<...<<<..<<<..[[....(((>>>..>>>.
...>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>
>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<
<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.
>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.
>>..<<<<<<....<.<........>.><<<<<<<<<<............
..........<<<.<<<<<<.........>>>>...<<<<<<<<<.....
....>>>>>>>>>....>>>>>>>>>>>>.>>>..<<<<.<<<<<.....
>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((.....
..<<<<<.....<<.........<<<.<<<<<<<<<<.......<<<<<.
<<....<<.........>>....>>.........<<......>>...>>>
>>...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...
>>>>>>><<<<<<.<<<..........)))....]]..............
..............>>>>>>>>>....>>>>>>.<<<<<<<<<<.<<...
...<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.>>.....>>>>>
><<<....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<
<...<<<<<....<<.....>>..>>>>>....((<<<<<<...<<....
<<<....>>>.............<<<<........>>>>.....>>....
>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<..
..>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<
<<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<<
<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>>
>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>..>.......
...>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>....<<<<.....<<<<<<<.<<...............<
<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<..<.........
...>.......>>>>>..>>>>>>.>>............<<<<<<<<<..
<<<.........>>>..<<<<<<<....<<<<.....>>>>......>>>
>>>>.......<<<..<<<<<<....<<<.....<<<<....>>>>....
.>>>.>>>>..>>>>>.........>>.>>>>>>>.....>>.>>>>>>>
..>>>>>>...>>>....<<<<<........>>>>>....(((((..{{{
........(((((.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<...>>>
>>>...<<<<<.....<<<<.....<..............>.........
.......<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>...
.>>>>>>>>>..>>>>>...<<......>>.........<<<<<<...<<
<<<<.......>>>>>>...........((......>>>>>>....<<<.
.<<<<....>>>>..>>>.<<<....>>>...))....(((((...(((.
.>>>>>>.))).)))))...]]]]..}})))))..........<<<<<<.
................>>>>>>.................<<<<.<<<<<<
..<.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>
>>>>..>...>>>>......<<<<<<<....>>>.>>>>........}}}
.))))).....<<<<<<.<..<<<..<.<<<<<.................
>>>>>.><<<<....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>.
..>>>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>
.>>>...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<.......
.<<<<<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<...
.<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>........
......>>>>..>>>>>>>>><<<<<.<.............>....<<.<
<<<<<<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>
>....>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ipx Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Resolution4.3 Å
Binding residue
(original residue number in PDB)
K237 G238 K241 S242 R244 W246 K247 K251 K252 R253 F254 L263 R264 W267 K270 R274 K299 R302 A303 L306
Binding residue
(residue number reindexed from 1)
K3 G4 K7 S8 R10 W12 K13 K17 K18 R19 F20 L29 R30 W33 K36 R40 K65 R68 A69 L72
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:8ipx, PDBe:8ipx, PDBj:8ipx
PDBsum8ipx
PubMed37491604
UniProtQ9H6F5|CCD86_HUMAN Coiled-coil domain-containing protein 86 (Gene Name=CCDC86)

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