Structure of PDB 8g5y Chain LS Binding Site BS01

Receptor Information

>8g5y Chain LS (length=176) Species: 9606 (Homo sapiens)

MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQ
LKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDL
TTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKI
KFPLPHRVLRRQHKPRFTTKRPNTFF

Ligand information

>8g5y Chain L5 (length=3721)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgacgccacgcaguuuua
uccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccu
auucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccg
ggcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggc
gcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcuca
ucagaccccagaaaagguguugguugauauagacagcaggacgguggcca
uggaagucggaauccgcuaaggaguguguaacaacucaccugccgaauca
acuagcccugaaaauggauggcgcuggagcgucgggcccauacccggccg
ucgccggcagucgagaguggacgggagcggcgggcccgcggacgcuacgc
cgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcgg
gcccggguggagccgccgcaggugcagaucuuggugguaguagcaaauau
ucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacag
caguugaacaugggucagucgguccugagagaugggcgagcgccguuccg
aagggacgggcgauggccuccguugcccucggccgaucgaaagggagucg
gguucagauccccgaauccggagcggagaugggcgccgcgaggcguccag
ugcgguaacgcgaccgaucccggagaagccggcgggagccccggggagag
uucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccga
gagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccggug
agcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgc
cgggccguacccauauccgcagcaggucuccaaggugaacagccucuggc
auguuggaacaauguagguaagggaagucggcaagccggauccguaacuu
cgggauaaggauuggcucuaagggcugguagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagagguguagaauaa
gugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcg
ggguccgccggcccugcgggccgccggugaaauaccacuacucugaucgu
uuuuucacugacccggugaggcgggggggcgagccccgaggggcucucgc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugacuggggcgguacaccugucaaacg
guaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgug
gagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacag
accgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagca
ggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaag
cguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauc
auugugaagcagaauucaccaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugauguguuguugccaugguaauccugcucaguacgagaggaaccgca
gguucagacauuugguguaugugcuuggcugaggagccaauggggcgaag
cuaccaucugugggauuaugacugaacgccucuaagucagaaucccgccc
aggcggaacgauacggcagcgccgcggagccucgguuggccucggauagc
cggucccccgcgggguccggugcggagugcccuucguccugggaaacggg
gcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguuc
guggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgg
gguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguca
gcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g5y mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.29 Å
• Binding residue (original residue number in PDB): K2 A3 S4 G5 R8 Y63 Q66 V67 F68 K70 P72 R74 S86 R87 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 A134 R139 F145 H146 D147 S148 H156 R157 V158 R160 R161 H163 P165 R166 T168 T169 K170 R171 P172 N173 T174 F175 F176
• Binding residue (residue number reindexed from 1): K2 A3 S4 G5 R8 Y63 Q66 V67 F68 K70 P72 R74 S86 R87 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 A134 R139 F145 H146 D147 S148 H156 R157 V158 R160 R161 H163 P165 R166 T168 T169 K170 R171 P172 N173 T174 F175 F176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g5y, PDBe:8g5y, PDBj:8g5y
• PDBsum: 8g5y
• PubMed: 37020024
• UniProt: Q02543|RL18A_HUMAN Large ribosomal subunit protein eL20 (Gene Name=RPL18A)