Structure of PDB 8fl6 Chain LL Binding Site BS01

Receptor Information

>8fl6 Chain LL (length=125) Species: 9606 (Homo sapiens)

SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV
EPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YRPDLRMAAIRRASAILRSQKPVMV

Ligand information

>8fl6 Chain L3 (length=3405)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggggcgcgggacauguggc
guacggaagacccgcuccccggcgccgcgggggcccaaguccuucugauc
gaggcccagcccguggacggugugaggccgguagcggcccccggcgcgcc
gggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcg
ggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaa
caaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaaga
gggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugucggcggcccggcggaucugg
gaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcg
gcggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaa
gguggcucgggcccgaguguuacagcccccccggcagcagcacucgccga
aucccggggccgagggaggucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuuacacggaccaaggagucuaacacgugcgcgagucgg
gggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcggccg
aggugggaucccgaggccucuccaguccgccgagggcgcaccaccggccc
gucucgcccgccgcgccggggagguggagcacgagcgcacguguuaggac
ccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacucu
gguggagguccguagcgguccugacgugcaaaucggucguccgaccuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaa
guuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcuu
uaaauggguaagaagcccggcucgcuggcguggagccgggcguggaaugc
gagugccuagugggccacuuuugcagaacuggcgcugcgggaugaaccga
acgccggguuaaggcgcccgaugccgacgcucaucagaccccaaaaggug
uugguugauauagacagcaggacgguggccauggaagucggaauccgcua
aggaguguguaacaacucaccugccgaaucaacuagcccugaaaauggau
ggcgcuggagcgucgggcccauacccggccgucgccggcagucgagagug
gacgggagcggcgcgcggacgcuacgccgcgacgaguaggagggccgcug
cggugagccuugaagccuagggcgcgggcccggguggagccgccgcaggu
gcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccg
aaguggagaaggguuccaugugaacagcaguugaacaugggucagucggu
ccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccgg
cccugaucgaaagggagucggguucagauccccgaauccggaguggcgga
gaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaa
gccggcgggagccccggggagaguucucuuuucuuugugaagggcagggc
gcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgu
cgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgg
gggagaggguguaaaucucgcgccgggccguacccauauccgcagcaggu
cuccaaggugaacagccucuggcauguuggaacaauguagguaagggaag
ucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcug
ggucggucgggcuggggcgcgaagcggggucccguggaucgccccagccg
gccggcgccuagcagccgacuuagaacuggugcggaccaggggaauccga
cuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgc
gaugugauuucugcccagugcucugaaugucaaagugaagaaauucaaug
aagcgcggguaaacggcaagugaacgagauucccacugucccuaccuacu
auccagcgaaaccacagccaagggcgggcuuggcggaaucagcggggaaa
gaagacccuguugagcuugacucuagucuggcacggugaaguuuuuucac
ugacccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgcc
ggccgggcgcgacccgcuccggggacagugccagguggggaguuugacug
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggaucuugug
gcggccaagcgagcgacgucgcugaugucggcucuuccuaucauugugaa
gcagaauucaccaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaugu
guuguugccaugguaauccugcucaguacgagaggaaccgcagguucaga
cauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccauc
ugugggauuaugacugaacgccucuaagucagaaucccgcccaggcggaa
cgauagcgccgcggagccucgguuggccucggauagccgguccccggggu
ccggugcggagugcccuucguccugggaaacggggcgcggccggagaggc
ggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgc
uaaaccauucguagacgaccugcuucugggucgggguuucguacguagca
gagcagcucccucgcugcgaucuauugaaagucagcccucgacacaaggg
uuugu

.........................<<<<<<.....<<....>>......
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>>>>>>..<<<..<<<<<...<<<<<<<<<..>>>>>.>>>>.....>>>
>>..<<<<<<<<<<...<<<<<<<<.<<<<<<<<<<....<<<<......
>>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>>
>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....<
<<<<..((((((>>>>>..>>>............................
......<<....>>...............<<<......>>>.........
.......................<<<<<<<<..<<<.<<...<<<<<<<<
.<<<.....<<<<<<<<<<<<<<<<<<.<<<<<.<<...<<<<<.<<...
>>>>>>>>>>>>>>>>>>...>>>>>>>>>>>>>>......>>>.>>>.>
>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<..
....<<<<<<..>>>>>>.......>>>>>>.>>>........>>>>>>.
.>>>>>>>>>>>............<<<<<<.<<<<<..>>>>>.<<<<<<
.<<<<.<<<<<<<<<<..<<<<<<<<<<<<<...........>.>>>>>>
>>>>>>...>>>>>>>.>>>...>>>>>>>>.>>..<<<<<<<<<.....
..>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>>...>>>
>>>>>..<<<<.....>>>><<<<<<....<<<<<<<<<<<<<..<<<..
.<<<<........>>>>.....>>>...<<....>>...<<<<..>>>>.
.<<<<<...<<<..<<<..((((.((((>>>..>>>....>>>>>.<<<<
<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<
<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>
>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>
>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<...
.<.<<<....>>>.><<.<<<<<<<...<<<.<<<<<<<<<...<<<.>>
>...>>>>>>>...<<<<<<<<<.<......>>>>>>>>>>....>>>>>
>>>>>>>..>>..<<<<.<<<<..>>>>.>>>>....<<<......>>>.
..<<<<<<<...<<<(((.......<<<<<.....<<........<<<.<
<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>...
......<<......>>...>>>>>...>>>>>>>>>>>>>..........
))).>>...>>>>>..>>>...>>>>>>><<<<<<.<<<..........)
))).)))).................>>>>>>>>>....>>>>>>.<.<<<
<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..
>.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<.
....<<<<<.<<...<<<<<....<<.....>>..>>>>>....((<<<<
<<...<<....<<<....>>>.............<<<<...........>
>>>...>>....>>>..<<<<<........>>>>>))<<<<....<<<<<
..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<<<<...
<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<
.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<
<<<.......>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>
>>..>..........>>.>>>.>>>>.>>>..>>.....<<......>>>
>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.<<....
...........<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<
.<<<<<<<<.<<<<<<<<<....<<<<<..>>>>>....>>>>>>>>>>>
>>>>>>......>>>>>..>>>>>>.>>............<<<<<<<<<.
.<<<.........>>>..<<<<<<<....<<<<.....>>>>......>>
>>>>>.......<<<..<<<<<<.<..<<<.....<<<<....>>>>...
..>>>>>>>>..>>>>>.......>>.>>>>>>>.....>>.>>>>>>>.
.>>>>>>....>>...<<<<<<......>>>>>>...<<<<<..<<<...
.....<<<<<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<.....>>>>>
...<<<<<.....<<<<................<<<<<<<<<<.......
>>>>>>>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<.>
>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.
......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<.<<<<<
.......>>>>.>>>>.<<<....>>>.>>)))].....<<<<<<<..<<
<..)))))).>>>>>>>>>>.........>>>>..>>>>>>>.......<
<<<<<...<<..>>...>>>>>>((...<<<<.<<<<<<..<.<.<<<<<
......>>>>>...>.>.<<<.....))..>>>.....>>>>>..>...>
>>>......<<<<<<<....>>>.>>>>........>>>.>>>>>.....
<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<<<
....<<<<....<<.<<<<<<.]]]..>>>>..>>.>>...>>>>...>>
>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>.>>
>>>>.<<<<<<.<<..<<<<....<<<........<<<<<.<<<<>>>>.
>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<<......>
>>>>>>>>>>...>>>>..>>>..............>>>>..>>>>>>>>
.<<<<<.<.............>....<<.<<<<<<<.<<.....<<<<..
..<<<<<......>>>>>...>>>>....>>....>>>.>>>>.>>..>>
>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl6 Principles of human pre-60 S biogenesis.
• Resolution: 2.62 Å
• Binding residue (original residue number in PDB): R11 N12 S15 K19 K22 R35 N36 S37 F38 R39 R66 R67 S68 R87 R94 H95 R98 K99 D105 R107 M108
• Binding residue (residue number reindexed from 1): R10 N11 S14 K18 K21 R34 N35 S36 F37 R38 R65 R66 S67 R86 R93 H94 R97 K98 D104 R106 M107

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:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0030425 dendrite
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0044297 cell body
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl6, PDBe:8fl6, PDBj:8fl6
• PDBsum: 8fl6
• PubMed: 37410842
• UniProt: P46779|RL28_HUMAN Large ribosomal subunit protein eL28 (Gene Name=RPL28)