Structure of PDB 8fl6 Chain LW Binding Site BS02

Receptor Information

>8fl6 Chain LW (length=86) Species: 9606 (Homo sapiens)

TKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSA
KAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKPK

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

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

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): T2 K3 G4 T5 S6 S7 F8 G9 K10 R11 R12 N13 K14 T15 H16 K25 H28 Q30 K31 G35 K36 R43 K44 R45 K46 Y47 N48 W49 K52 R55 R56 T58 T59 Y71
• Binding residue (residue number reindexed from 1): T1 K2 G3 T4 S5 S6 F7 G8 K9 R10 R11 N12 K13 T14 H15 K24 H27 Q29 K30 G34 K35 R42 K43 R44 K45 Y46 N47 W48 K51 R54 R55 T57 T58 Y70

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding
• GO:0097371 MDM2/MDM4 family protein binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:1901798 positive regulation of signal transduction by p53 class mediator

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fl6, PDBe:8fl6, PDBj:8fl6
• PDBsum: 8fl6
• PubMed: 37410842
• UniProt: P61927|RL37_HUMAN Large ribosomal subunit protein eL37 (Gene Name=RPL37)