Structure of PDB 8ir3 Chain E Binding Site BS01

Receptor Information

>8ir3 Chain E (length=98) Species: 9606 (Homo sapiens)

KSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKS
EIEYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIR

Ligand information

>8ir3 Chain 2 (length=3541)

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
gacgcccgccacgcaguuuuauccgguaaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggcccuc
ggccgaucgaaagggagucggguucagauccccgaauccggaguggcgga
gaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaa
gccggcgggagccccggggagaguucucuuuucuuugugaagggcagggc
gcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgu
cgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgg
gggagaggguguaaaucucgcgccgggccguacccauauccgcagcaggu
cuccaaggugaacagccucuggcauguuggaacaauguagguaagggaag
ucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcug
ggucggucgcggccggcgccuagcagccgacuuagaacuggugcggacca
ggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcg
gguguugacgcgaugugauuucugcccagugcucugaaugucaaagugaa
gaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucuua
agguagccaaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaaguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugggcgguacaccugucaaacgguaacgcaggugucaaggcgagcu
cagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuuga
ucuugauuuucaguacgaauacagaccgugaaagcggggccucacgaucc
uucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacagg
guggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuuc
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagugc
ccuucguccugggaaacggggcgcggccggagaggcggccgcccccucgc
ccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguag
acgaccugcuucugggucgggguuucguacguagcagagcagcucccucg
cugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ir3 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): L29 G30 Y31 K32 Q33 N51 P53 A54 R56 Y88 Y89 V91 C92
• Binding residue (residue number reindexed from 1): L21 G22 Y23 K24 Q25 N43 P45 A46 R48 Y80 Y81 V83 C84

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
• GO:0031640 killing of cells of another organism
• GO:0050829 defense response to Gram-negative bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• 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:8ir3, PDBe:8ir3, PDBj:8ir3
• PDBsum: 8ir3
• PubMed: 37491604
• UniProt: P62888|RL30_HUMAN Large ribosomal subunit protein eL30 (Gene Name=RPL30)