Structure of PDB 8g5y Chain LT Binding Site BS01

Receptor Information

>8g5y Chain LT (length=159) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFMA

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): T2 N3 T4 K5 G6 K7 R8 R9 G10 R12 Y13 S16 F19 H22 G23 K35 D41 K43 G46 T47 Q49 G51 H54 K55 Y57 H58 G59 K60 T61 T68 Q69 H70 A71 N77 K78 V80 K81 K83 L85 K87 R88 N90 R92 K97 K100 S101 R102 F105 R108 V109 N112 D113 W125 V126 L128 K129 R130 F140 R142
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 G9 R11 Y12 S15 F18 H21 G22 K34 D40 K42 G45 T46 Q48 G50 H53 K54 Y56 H57 G58 K59 T60 T67 Q68 H69 A70 N76 K77 V79 K80 K82 L84 K86 R87 N89 R91 K96 K99 S100 R101 F104 R107 V108 N111 D112 W124 V125 L127 K128 R129 F139 R141

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:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g5y, PDBe:8g5y, PDBj:8g5y
• PDBsum: 8g5y
• PubMed: 37020024
• UniProt: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)