Structure of PDB 8flb Chain LL Binding Site BS01

Receptor Information

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

SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV
EPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YRPDLRMAAIRRASAILRSQKPVMV

Ligand information

>8flb Chain L3 (length=3420)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggggcgcgggacauguggc
guacggaagacccgcuccccggcgccgcgggggcccaaguccuucugauc
gaggcccagcccguggacggugugaggccgguagcggcccccggcgcgcc
gggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcg
ggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaa
caaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaaga
gggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugucggcggcccggcggaucugg
gaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcg
gcggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaa
gguggcucgggcccgaguguuacagcccccccggcagcagcacucgccga
aucccggggccgagggaggucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaag
uuuaaauggguaagaagcccggcucgcuggcguggagccgggcguggaau
gcgagugccuagugggccacuuuugguaagcagaacuggcgcugcgggau
gaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccg
aaaagguguugguugauauagacagcaggacgguggccauggaagucgga
auccgcuaaggaguguguaacaacucaccugccgaaucaacuagcccuga
aaauggauggcgcuggagcgucgggcccauacccggccgucgccggcagu
cgagaguggacgggagcggcgcgcggacgcuacgccgcgacgaguaggag
ggccgcugcggugagccuugaagccuagggcgcgggcccggguggagccg
ccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuu
gaaggccgaaguggagaaggguuccaugugaacagcaguugaacaugggu
cagucgguccugagagaugggcgagcgccguuccgaagggacgggcgaug
gccuccggcccugaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgggcuggggcgcgaagcggggucccguggaucgc
cccagccggccggcgccuagcagccgacuuagaacuggugcggaccaggg
gaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggu
guugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaugaagcgcggguaaacggcaagugaacgagauucccacuguccc
uaccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauc
agcggggaaagaagacccuguugagcuugacucuagucuggcacggugaa
guuuuuucacugacccggugaggcggggggcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuguacaccugucaaacgguaacgcagguguccuaaggcgagc
ucagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuug
aucuugauuuucaguacgaauacagaccgugaaagcggggccucacgauc
cuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacag
ggaucuuguggcggccaagcgagcgacgucgcuuuuuggaugucggcucu
uccuaucauugugaagcagaauucaccaagcguuggauuguucacccacu
aauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuua
cccuacugaugauguguuguugccaugguaauccugcucaguacgagagg
aaccgcagguucagacauuugguguaugugcuuggcugaggagccaaugg
ggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaau
cccgcccaggcggaacgauagcgccgcggagccucgguuggccucggaua
gccgguccccgggguccggugcggagugcccuucguccugggaaacgggg
cgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8flb Principles of human pre-60 S biogenesis.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): R11 S15 K19 K22 K33 R35 N36 S37 F38 R39 K47 R66 R67 S68 K84 N85 R87 S92 R94 H95 R98 K99 N100 D105 R107 M108 R112
• Binding residue (residue number reindexed from 1): R10 S14 K18 K21 K32 R34 N35 S36 F37 R38 K46 R65 R66 S67 K83 N84 R86 S91 R93 H94 R97 K98 N99 D104 R106 M107 R111

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