Structure of PDB 8fkz Chain LL Binding Site BS01

Receptor Information

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

SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV
EPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YRPDLRMAAIRRASAILRSQKPVMV

Ligand information

>8fkz Chain L3 (length=2833)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucaaacacggaccaaggagucuaacacgugcgc
gagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggcc
gcggccgaggugggaucccgaggccgccgagggcgcaccaccggcccguc
ucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccg
aaagauggugaacuaugccugggcagggcgaagccagaggaaacucuggu
ggagguccguagcguccgaccuggguauaccaucuaguagcugguucccu
ccgaaguuucccucaggauagcuggcgcucuccgcaguuuuauccggggg
uaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugccu
agugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacg
ccggguuaaggcgcccgaugccgacgcucaucagaccagaaaagguguug
guugauauagacagcaggacgguggccauggaagucggaauccgcuaagg
aguguguaacaacucaccugccgaaucaacuagcccugaaaauggauggc
gcuggagcgucgggcccauacccggccgucgccggcagugacgcuacgcc
gcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcggg
cccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauu
caaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagc
aguugaacaugggucagucgguccugagagaugggcgagcgccguuccga
agggacgggcgauggccuccggcccucgaucgaaagggagucggguucag
auccccgaauccggaguggcggagaugggcgccgcgaggcguccagugcg
guaacgcgaccgaucccggagaagccggcgggagccccggggagaguucu
cuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagaga
ggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagcu
cucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccggg
ccguacccauauccgcagcaggucuccaaggugaacagccucuggcaugu
uggaacaauguagguaaggggcucuaagggcugggucggucgggcugggg
cgcgaagcggggucccguggaucgccccagccggccggcgccuagcagcc
gacuuagaacugcaucgcgaaggcccgggguguugacgcgauguuguccc
uaccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauc
agacccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgcc
ggccgggcgcgacccgcuccggggcuucugaccuuuuggguuuuaagcag
gagggcuuguggcggccaagcgagcgacgucgcuuuuugcggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggcuacugaugauguguuguugccaugguaauccugc
ucaguacgagaggaaccgcagguucagacauuugguguaugugcuuggcu
gaggagccaauggggcgaagcuaccaucugugggauuaugacugaacgcc
ucuaagucagaaucccgcccaggcggaacgauagcgccgcggagccucgg
uuggccucggauagccgguccccgggguccggugcggagugcccuucguc
cugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacg
caccgcacguucguggggaaccuggcgcuaaaccauucguagacgaccug
cuucugggucgggguuucguacguagcagagcagcucccucgcugcgauc
uauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkz Principles of human pre-60 S biogenesis.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): W7 R11 N12 S15 K19 K22 K33 R35 N36 S37 F38 R39 R66 R67 S68 K84 R87 H95 R98 K99 N100 D105 R107 M108 R112
• Binding residue (residue number reindexed from 1): W6 R10 N11 S14 K18 K21 K32 R34 N35 S36 F37 R38 R65 R66 S67 K83 R86 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:8fkz, PDBe:8fkz, PDBj:8fkz
• PDBsum: 8fkz
• PubMed: 37410842
• UniProt: P46779|RL28_HUMAN Large ribosomal subunit protein eL28 (Gene Name=RPL28)