Structure of PDB 8ir1 Chain p Binding Site BS01

Receptor Information

>8ir1 Chain p (length=225) Species: 9606 (Homo sapiens)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNA
LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>8ir1 Chain 2 (length=3369)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacggcaaaucgguc
guccgaccuggguauaggggcgaaacuaaucaccaucuaguagcugguuc
ccuccgaaguuuccccaggauagcuggcgcucucgcgcaguuuuauccgg
uaaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcg
uggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcug
cgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucag
acccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggcagucgagaguggacgggagcggcggcccggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaacgaucgaaagggagucggguucagauccccgaauccggaguggcgg
agaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggaga
agccggcgggagccccggggagaguucucuuuucuuugugaagggcaggg
cgcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcg
ucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccg
ggggagaggguguaaaucucgcgccgggccguacccauauccgcagcagg
ucuccaaggugaacagccucuggcauguuggaacaauguagguaagggaa
gucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcu
guagcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaa
uuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugau
uucaaagugaagaaaucaaugaaggaguaacuaugacucucgguagccaa
augaacgagauucccacugucccuaccuacuauccagcgaaaccacagcc
aagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcu
ugacucuagucuggcacggugaaguuuuuucacugacccggugaggcggc
cgcuccggggacagugccagguggggaguuugagggcgguacaccuguca
aacgguaacgcagguguccuaaggcgagcucagggaggacagaaaccucc
cguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaau
acagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuua
agcaggaggugucagaaaaguuacagggauaggcuuguggcggccaagcg
uucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucau
ugugaagcagaauucaccaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacggcagcgccgcggagccucgguuggccucggauagccgg
ucccccgccgggguccggugcggagugcccuucguccugggaaacggggc
gcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgu
ggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggg
uuucguacguagcagagcagcucccucgcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ir1 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): F25 A26 L28 K29 I30 K31 R32 L33 R34 F37 R47 Y51 H58 K59 R62 Y65 R66 I69 R73 M74 R76 R96 G97 I98 N99 P103 K107 L111 Q116 I117 K124 A128 N131 L147 N151 R157 K164 K165 R166 E188 K202 N206 K212 L213 S214 S215 P216 R217 G218 K223 R242
• Binding residue (residue number reindexed from 1): F2 A3 L5 K6 I7 K8 R9 L10 R11 F14 R24 Y28 H35 K36 R39 Y42 R43 I46 R50 M51 R53 R73 G74 I75 N76 P80 K84 L88 Q93 I94 K101 A105 N108 L124 N128 R134 K141 K142 R143 E165 K179 N183 K189 L190 S191 S192 P193 R194 G195 K200 R219

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ir1, PDBe:8ir1, PDBj:8ir1
• PDBsum: 8ir1
• PubMed: 37491604
• UniProt: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)