Structure of PDB 8g5z Chain LY Binding Site BS02

Receptor Information

>8g5z Chain LY (length=134) Species: 9606 (Homo sapiens)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>8g5z Chain L5 (length=3687)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccgcgggggaccgucccccgaccggcgaccggccgccg
ccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggc
ugggaaggcccggcggggaagguggcucgggggcccccgaguguuacagc
ccccccggcagcagcacucgccgaaucccggggccgagggagcgagaccc
gucgccgcgcucuccccccugggggggccgggccaccccucccacggcgc
gaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccgu
cgggcccggggggccacgcgcgcgucccccgaagagggggacggcggagc
gagcgcacggggucggcggcgacgucggcuacccacccgacccgucuuga
aacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacgaa
agccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgagg
ugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccguc
ucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccg
aaagauggugaacuaugccugggcagggcgaagccagaggaaacucuggu
ggagguccguagcgguccugacgugcaaaucggucguccgaccuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaaguu
ucccucaggauagcuggcgcucucgcagacccgaacgcaguuuuauccgg
uaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucu
caaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcgu
ggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugc
gggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucaga
ccccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggcagucgagaguggacgggagcggcgggccggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaagggacgggcgauggccuccguugcccucggccgaucgaaagggagu
cggguucagauccccgaauccggagcggagaugggcgccgcgaggcgucc
agugcgguaacgcgaccgaucccggagaagccggcgggagccccggggag
aguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcccc
gagagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgg
ugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgc
gccgggccguacccauauccgcagcaggucuccaaggugaacagccucug
gcauguuggaacaauguagguaagggaagucggcaagccggauccguaac
uucgggauaaggauuggcucuaagggcugggucggucgcggccggcgccu
agcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaauu
aaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuu
cugcccagugcucugaaugucaaagugaagaaauucaaugaagcgcgggu
aaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguca
ucuaauuagugacgcgcaugaauggaugaacgagauucccacugucccua
ccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucag
cggggaaagaagacccuguugagcuugacucuagucuggcacggugaaga
gacaugagagguguagaauaagugggaggcccgggccgccggugaaauac
cacuacucugaucguuuuuucacugacccggugaggcgggggggcgagcc
ccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccggucccccgccgggguccggugcggagugcccuu
cguccugggaaacggggcgcggccggagaggcggccgcccccucgcccgu
cacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacga
ccugcuucugggucgggguuucguacguagcagagcagcucccucgcugc
gaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g5z mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.64 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 P5 T8 S9 R11 K13 N14 R15 H18 K28 S31 P33 K36 R39 R45 S46 R59 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 P5 T8 S9 R11 K13 N14 R15 H18 K28 S31 P33 K36 R39 R45 S46 R59 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g5z, PDBe:8g5z, PDBj:8g5z
• PDBsum: 8g5z
• PubMed: 37020024
• UniProt: P61254|RL26_HUMAN Large ribosomal subunit protein uL24 (Gene Name=RPL26)