Structure of PDB 8g61 Chain LX Binding Site BS02

Receptor Information

>8g61 Chain LX (length=118) Species: 9606 (Homo sapiens)

KIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMK
KIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYV
RLAPDYDALDVANKIGII

Ligand information

>8g61 Chain L5 (length=3657)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccgcgggggaccgucccccgaccggcgaccggccgccg
ccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggc
ugggaaggcccggcggggaagguggcucgggggccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccggggggccacgcgcgcgucccccgaagagggggacggcggagcg
agcgcacggggucggcggcgacgucggcuacccacccgacccgucuugaa
acacggaccaaggagucuaacacgugcgcgagucgggggcucgcacgaaa
gccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgaggu
gggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgucu
cgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccga
aagauggugaacuaugccugggcagggcgaagccagaggaaacucuggug
gagguccguagcgguccugacgugcaaaucggucguccgaccuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaaguuu
cccucaggauagcuggcgcucucgcagacccgaacgcaguuuuauccggu
aaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucuc
aaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucgagaguggacgggagcggccccgcggacgcuacgccgcgacgag
uaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggug
gagccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgag
aacuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaac
augggucagucgguccugagagaugggcgagcgccguuccgaagggacgg
gcgauggccuccguugcccucggccgaucgaaagggagucggguucagau
ccccgaauccggagcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugguagcagccgacuuagaacuggugcggaccag
gggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgg
guguugacgcgaugugauuucugcccagugcucugaaugucaaagugaag
aaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccgggccgccggugaaauaccacuacucugaucguuuuuucacugacccg
gugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcg
cccggccgcgcgccggccgggcgcgacccgcuccggggacagugccaggu
ggggaguuugacuggggcgguacaccugucaaacgguaacgcaggugucc
uaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaa
agcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcgggg
ccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaa
guuaccacagggauaacuggcuuguggcggccaagcguucauagcgacgu
cgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugauguguuguug
ccaugguaauccugcucaguacgagaggaaccgcagguucagacauuugg
uguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggga
uuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauacg
gcagcgccgcggagccucgguuggccucggauagccggucccccgccggg
guccggugcggagugcccuucguccugggaaacggggcgcggccggagag
gcggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggc
gcuaaaccauucguagacgaccugcuucugggucgggguuucguacguag
cagagcagcucccucgcugcgaucuauugaaagucagcccucgacacaag
gguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g61 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): P44 T45 F46 R47 R48 P49 K50 T51 R53 L54 R56 Q57 K59 Y60 R62 T83 S85 K89 N105 K106 H107 K123 N125 T126 L127 I128 P130 K134 K135 Y137 R139
• Binding residue (residue number reindexed from 1): P6 T7 F8 R9 R10 P11 K12 T13 R15 L16 R18 Q19 K21 Y22 R24 T45 S47 K51 N67 K68 H69 K85 N87 T88 L89 I90 P92 K96 K97 Y99 R101

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045296 cadherin binding
• GO:1904841 TORC2 complex binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g61, PDBe:8g61, PDBj:8g61
• PDBsum: 8g61
• PubMed: 37020024
• UniProt: P62750|RL23A_HUMAN Large ribosomal subunit protein uL23 (Gene Name=RPL23A)