Structure of PDB 8ipd Chain K Binding Site BS01

Receptor Information
>8ipd Chain K (length=102) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFA
PYERRAMELLKVSKDKRALKFIKKRVGTHIRAKRKREELSNVLAAMRKAA
AK
Ligand information
>8ipd Chain 2 (length=3485) [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
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
aauucaaugaagcgcggguaaacggcgguuaagaacgagauucccacugu
cccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggcgga
aucagcggggaaagaagacccuguugagcuugacucuagucuggcacggu
gaaguuuuuucacugacccggugaggcgggggggcgagccccgaggggcu
cucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccg
cuccggggacagugccagguggggaguuuccugucgcagguguccuaagg
cgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcuc
gcuugaucuugauuuuuacgaauacagaccgugaaagcggggccgauccu
ucugaccuuuuggguuuuaagcaggagguaaguuaccacagggauaggcu
uguggcggccaagcguucauagcgacgucgcuuuuugauccuucgauguc
ggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguuca
cccacuaauagggaacgugagcuggguuuagaccgucgugagacagguua
guuuuacccuacugaugauguguuguugccaugguaauccugcucaguac
gagaggaaccgcagguucagacauuugguguaugugcuuggcugaggagc
caauggggcgaagcuaccaucugugggauuaugacugaacgccucuaagu
cagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgguu
ggccucggauagccggucccccgccgggguccggugcggagugcccuucg
uccugggaaacggggcgcggccggagaggcggccgcccccucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcucccucgcugcga
ucuauugaaagucagcccucgacacaaggguuugu
.........................<<<<<<<....<......>.....>
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>>>>>>..[[[..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<<....>>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<.......<<
....<<<<.<<<..<<<<..>>>>>>>>>>>>>......>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
<<<<<...<<..<<<..<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>.>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<.<<<<<..<<<<....<<......>>....>>>
>..>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<..
.....>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>>...
>>>>>>>>..<<<<.......>>>><<<<<<....<<<<<<<<<<<<<..
<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<<
<......>>>>>>>..<<<<<...<<<..<<<..(((...(((>>>..>>
>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>
>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....
<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>
>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>..
>.>>..<<<<<<....<.<........>.><<.<<<<<<<..........
............<<<.<<<<<<<<<...>>>>>>>...<<<<<<<<<...
......>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<...
..>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((...
....<<<<<.....<<.........<<<.<<<<<<<<<<.......<<<<
<.<<<...<<.........>>...>>>.........<<......>>...>
>>>>...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>.
..>>>>>>><<<<<<.<<<..........)))...)))............
................>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<.
.....<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>
>>><<.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<
.<<...<<<<<....<<.....>>..>>>>>....((<<<<<<...<<..
..<<<....>>>..........<<.<<<<...<<...>>...>>>>>>..
....>>....>>>..<<<<<........>>>>>))<<<<....<<<<<..
.<<<<.<<....>>.>>>>...<<<....>>>...<..<<<<<<<...<<
<<<<<<<<<<<<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<
<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<
<.......>>>>>>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>
..>..........>>.>>>.>>>>.>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.<<......
.........<<<<<....<....>.....>>>>><<.<<<<<<<<<<<..
<............>.......>>>>>..>>>>>>.>>............<
<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>
>......>>>>>>>.......<<<..<<<<<<....<<<.....<<<<..
..>>>>.....>>>.>>>>..>>>>>.........>>.>>>>>>>.....
>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....
(((((..[[[........(((((.[[((((..<<<<..<<<<<<<<<.<<
<<<<...>>>>>>...<<<<<.....<<<<.....<<............>
>................<.<<<<<<<<.......>>>>>>>>.>..>>>>
..>>>>>....>>>>>>>>>...>>>>...<<......>>..........
<<<<<...<<<<<<.......>>>>>>...........((......>>>>
>.....<<<..<<<<....>>>>..>>>.<<<....>>>...)).....(
(((...(((..>>>>>>.))).))))....))))..]]))))).......
...<<<<<<.................>>>>>>.................<
<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<........
.>>>.....>>>>>..>...>>>>......<<<<<<<....>>>.>>>>.
.......]]].))))).....<<<<<<.<..<<<..<.<<<<<.......
..........>>>>>.><<<<....<<<<....<<.<<<<<<.]]]..>>
>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>>>
>>...>>>>>.>>>...>.>>>>>>.....<<<<<<..<<..<<<<....
<<<........<<<<<.<<<<....>>>>.>>>>>.......>>>...<<
<..<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>
>>..............>>>>..>>.>>>>>><<<<<.<............
.>....<<.<<<<<<<.<<.....<<<<.<..<<<<<......>>>>>..
>>>>>....>>....>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ipd Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
R4 H15 H26 S27 R28 R29 R30 G31 R32 L33 T34 R41 R68 R76 R82 K84 R85
Binding residue
(residue number reindexed from 1)
R3 H14 H25 S26 R27 R28 R29 G30 R31 L32 T33 R40 R67 R75 R81 K83 R84
Enzymatic activity
Enzyme Commision number ?
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:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0016020 membrane
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
GO:0045202 synapse
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8ipd, PDBe:8ipd, PDBj:8ipd
PDBsum8ipd
PubMed37491604
UniProtQ9Y3U8|RL36_HUMAN Large ribosomal subunit protein eL36 (Gene Name=RPL36)

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