Structure of PDB 8fl6 Chain LZ Binding Site BS02

Receptor Information

>8fl6 Chain LZ (length=50) Species: 9606 (Homo sapiens)

SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL

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): S2 S3 H4 K5 K10 L13 K34 R36 Y37 S39 R41 R42 H43 W44 R45 K48 L49
• Binding residue (residue number reindexed from 1): S1 S2 H3 K4 K9 L12 K33 R35 Y36 S38 R40 R41 H42 W43 R44 K47 L48

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0002227 innate immune response in mucosa
• GO:0006412 translation
• GO:0019731 antibacterial humoral response
• GO:0050830 defense response to Gram-positive bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005615 extracellular space
• 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: P62891|RL39_HUMAN Large ribosomal subunit protein eL39 (Gene Name=RPL39)