Structure of PDB 8fl3 Chain L5 Binding Site BS01

Receptor Information

>8fl3 Chain L5 (length=168) Species: 9606 (Homo sapiens)

ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVR
SFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFG
IQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRIS
KEEAMRWFQQKYDGIILP

Ligand information

>8fl3 Chain L3 (length=3494)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucuugaaacacggaccaaggagucuaacacgug
cgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaag
gccgcggccgaggugggaucccgaggcccgccgagggcgcaccaccggcc
cgucucgcccgccgcgccggggagguggagcacgagcgcacguguuagga
cccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacuc
ugguggagguccguagcgguccugacgugcaaaucggucguccgaccugg
guauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccga
aguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcg
aaugauuagaggucuuggggccggaucucaaccuauucucggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagugacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgauggccuccggcccucgaucgaaagggagucggguucagauccc
cgaauccggaguggcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugggucggucgggcuggggcgcgaagcggggucc
cguggaucgccccagccggccggcgccuagcagccgacuuagaacuggug
cggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcc
cgggguguugacgcgaugugauuucugcccagugcucugaaugucaaagu
gaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucuc
uuaagguagccaaaugccucgucaugugacgcgcaugaauggaugaacga
gauucccacugucccuaccuacuauccagcgaaaccacagccaagggaac
gggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucua
gucuggcacggugaagagacaugagagguguagaauaagugggaggcggc
cgccggugaaauaccacuacucugaucguuuuuucacugacccggugagg
cggggggcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgac
ccgcuccggggacagugccagguggggaguuugguacaccugucaaacgg
uaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugg
agcagaagggcaaaagcucgcuugaucuugauuuuguacgaauacagacc
gugaaagcggggccucacccuucugaccuuuuggguuuuaagcaggagga
aguuaccacagggauaacuggcuuguggcggccaagcgagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauagcgccg
cggagccucgguuggccucggauagccgguccccgggguccggugcggag
ugcccuucguccugggaaacggggcgcggccggagaggcggccgcccccu
cgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucg
uagacgaccugcuucugggucgggguuucguacguagcagagcagcuccc
ucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl3 Principles of human pre-60 S biogenesis.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 G27 S51 A53 S59 F60 I62 H71 N97 N98 D101 T102 N104 G106 F107 G108 Q110 G127 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K11 C13 N15 C17 G19 S43 A45 S51 F52 I54 H63 N89 N90 D93 T94 N96 G98 F99 G100 Q102 G119 D121 Y123 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006605 protein targeting
• GO:0010628 positive regulation of gene expression
• GO:0032092 positive regulation of protein binding
• GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
• GO:0034504 protein localization to nucleus
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl3, PDBe:8fl3, PDBj:8fl3
• PDBsum: 8fl3
• PubMed: 37410842
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)