Structure of PDB 8g5z Chain LT Binding Site BS01

Receptor Information

>8g5z Chain LT (length=159) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFMA

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): T2 N3 T4 K5 G6 K7 R8 R9 G10 R12 Y13 M14 S16 R17 F19 H22 G23 K35 D41 K43 G46 T47 Q49 K50 G51 H54 K55 Y57 H58 G59 K60 T61 T68 Q69 H70 A71 N77 K78 V80 K81 K83 L85 K87 R88 N90 R92 K97 S101 F105 R108 V109 K110 D113 K116 K120 W125 V126 L128 K129 R130 P132 F140 V141 R142
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 G9 R11 Y12 M13 S15 R16 F18 H21 G22 K34 D40 K42 G45 T46 Q48 K49 G50 H53 K54 Y56 H57 G58 K59 T60 T67 Q68 H69 A70 N76 K77 V79 K80 K82 L84 K86 R87 N89 R91 K96 S100 F104 R107 V108 K109 D112 K115 K119 W124 V125 L127 K128 R129 P131 F139 V140 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:8g5z, PDBe:8g5z, PDBj:8g5z
• PDBsum: 8g5z
• PubMed: 37020024
• UniProt: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)