Structure of PDB 8fkz Chain LG Binding Site BS01

Receptor Information

>8fkz Chain LG (length=127) Species: 9606 (Homo sapiens)

GGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGLPAAGVGDMVMA
TVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMK
GSAITGPVAKECADLWPRIASNAGSIA

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): R15 S17 G19 P21 A24 S41 L52 R85 K86 F95
• Binding residue (residue number reindexed from 1): R9 S11 G13 P15 A18 S35 L39 R72 K73 F82

Gene Ontology

Molecular Function

• GO:0001223 transcription coactivator binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0070180 large ribosomal subunit rRNA binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006610 ribosomal protein import into nucleus
• GO:0008284 positive regulation of cell population proliferation
• GO:0010628 positive regulation of gene expression
• GO:0032986 protein-DNA complex disassembly
• GO:0050821 protein stabilization
• GO:0070314 G1 to G0 transition
• GO:0072717 cellular response to actinomycin D
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1903450 regulation of G1 to G0 transition
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• 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: P62829|RL23_HUMAN Large ribosomal subunit protein uL14 (Gene Name=RPL23)