Structure of PDB 8jdm Chain o Binding Site BS01

Receptor Information

>8jdm Chain o (length=86) Species: 9606 (Homo sapiens)

TKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSA
KAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKPK

Ligand information

>8jdm Chain D (length=3512)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgccgggcccgggucuucccggagucggguugcuugggaaugcagcc
caaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccga
uagucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagag
uucaagagggcgugaaaccguuaagagguaaacgggugggguccgcgcag
uccgcccggaggauucaacccggcggcggguccggccgugucggcgggcg
gaucuuucccgggggaccgucccccgaccggcgaccggccgccgccgggc
gcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaa
ggcccggcggggaagguggcucgggggcccccgaguguuacagccccccc
ggcagcagcacucgccgaaucccggggccgagggagcgagacccgucgcc
gcgcucuccccccugggggggccgggccaccccucccacggcgcgaccgc
ucggggcggacuguccccagugcgccccgggcgggucgcgccgucgggcc
cggggggccacgcgcgcgucccgggacggcggagcgagcgcacggggucg
gcggcgacgucggcuacccacccgacccgucuugaaacacggaccaagga
gucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgca
augaaggugaaggccggcgcgcucgccggccgaggugggaucccgaggcc
ucuccaguccgccgagggcgcaccaccggcccgucucgcccgccgcgccg
gggagguggagcacgagcgcacguguuaggacccgaaagauggugaacua
ugccugggcagggcgaagccagaggaaacucugguggagguccguagcgg
uccugacgugcaaaucggucguccgaccuggguauaggggcgaaagacua
aucgaaccaucuaguagcugguucccuccgaaguuucccucaggauagcu
ggcgcucucgcagacccgacccgccacgcaguuuuauccgguaaagcgaa
ugauuagaggucuuggggccgaucucaaccuauucucaaacuuuaaaugg
guaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugcc
uagugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaac
gccggguuaaggcgcccgaugccgacgcucaucagaccccagaaaaggug
uugguugauauagacagccgaaucaacuagcccugaaaauggauggcgcu
ggagcgucgggcccauacccggccgucgccggcagucgagaguggacggg
agccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagc
cuugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucu
uggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggag
aaggguuccaugugaacagcaguugaacaugggucagucgguccugagag
augggcgagcgccguuccgaagggacgggcgauggccuccguugcccucg
gccgaucgaaagggagucggguucagauccccgaauccggaguggcggag
augggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaag
ccggcgggagccccggggagaguucucuuuucuuugugaagggcagggcg
cccuggaauggguucgccccgagagaggggcccgugccuuggaaagcguc
gcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccggg
ggagaggguguaaaucucgcgccgggccguacccauauccgcagcagguc
uccaaggugaacagccucuggcauguuggaacaauguagguaagggaagu
cggcaagccggauccguaacuucgggauaaggauuggcucuaagggcugc
agccgacuuagaacuggugcggaccaggggaauccgacuguuuaauuaaa
acaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaa
cggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucu
aauuagugacgcgcaugaauggaugaacgagauucccacugucccuaccu
acuauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcgg
ggaaagaagacccuguugagcuugacucuagucuggcacggugaagagac
guuuuuucacugacccggugaggcgggggggcgagcucucgcuucuggcg
ccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacagu
gccagguggggaguuugacuggggcgguacaccugucaaacgguaacgca
gguguccuaaggcgagcucagggaggacagaaaccucccguggagcagaa
gggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaa
agcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggugu
cagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucaua
gcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugugaa
gcagaauucaccaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaugu
guuguugccaugguaauccugcucaguacgagaggaaccgcagguucaga
cauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccauc
ugugggauuaugacugaacgccucuaagucagaaucccgcccaggcggaa
cgauacggcagcgccgcggagccucgguuggccucggauagccggucccc
ccgggguccggugcggagugcccuucguccugggaaacggggcgcggccg
gagaggcggccgcccccucgcccgucacgcaccgcacguucguggggaac
cuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgua
cguagcagagcagcucccucgcugcgaucuauugaaagucagcccucgac
acaaggguuugu

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>>>>..<<<<<<<<<....<<<<.<<<........<<<<<<<<....<<<
<......>>>>.....((......<<<.....))>>>...>.>>>>>>>.
..>>>.>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>
>.....(((((..<<<<<<)))))..]]].....................
.............<<....>>...............<<<......>>>..
................................<<<<<<<<..<<<.<...
.<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<.<...<<<<.<<<<<
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.....>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<.
.<<<.<<.<<<<......<<<<<<<<..>>>>>>>>.......>>>>.>>
>>>........>>>>>>..>>>>>>>>>>>....................
<<<<<..<<<<<<..>>>>>>.<<<<<<.<<<<.<<<<<<<<<<<.<<<<
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.>>>>>>>>.>>..<<<<<<<..>>>>>.>>.....>>>>>.....>>>.
>>>>>....>>>>...>>>>>>>>..<<<<........>>>><<<<<<..
..<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>>>...
<<....>>...<<<<<<<<....>>>>>>>>..<<<<<...<<<..<<<.
.((((.((((>>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>
>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<
<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<.
.<<.<<........>>>>.>>>....>>>>>>>>>...<<.......>>.
.....>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.
<<<<<<<....................<<<.<<<<<<<<<...<<<....
<<<..<.<<<<...<<<<....>>>>.>>>>.>..>>>..>.>>...>>>
>>>>...<<<<<<<<<.........>>>>>>>>>....>>>>>>>>>>>>
..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...
<<<<<<<...<<<(((.......<<<<<.....<<..........<<<.<
<<<<<<<<<............>>>>>>>>>>>>>..........))).>>
...>>>>>..>>>...>>>>>>><<<<<<.<<<..........)))).))
))...............>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<
......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>
>>>><<.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<
<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<.
...<<<....>>>..........<<.<<<<<..<.....>..>>>>>>>.
.....>>....>>>..<<<<<........>>>>>))<<<<....<<<<<.
.<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<<<<...<
<<<<<<<<<<<.<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.
<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<
<<.......>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>
>..>..........>>.>>>.>>>>.>>>..>>.....<<......>>>>
>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.<<.....
....<.....<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<..
>>>>..>>>>>>.>>............<<<<<<<<<..<<<.........
>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<
<<..<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>
>>>><<<<<<.......>>>>>>........<...........<<<<<..
.....>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>
>>..>>>>>>....>>....<<<<<........>>>>>....[[[[[..{
{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<<.
.>>>>>>>>>...<<<<<.....<<<<...<.<<..>>>...........
....<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>....>>
>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>
>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(
((>>....>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<...
.>>>.>>)))]......((((((..(((..>>>>>>.)))))))))....
......]]]]..}}]]]].......<<.<.<.<<<<<<...<<.......
>>...>>>>>>...>>.>.>........<<<<.<<<<<<..<.<.<<<<<
......>>>>>...>.>.<<<.........>>>.....>>>>>..>...>
>>.>.....<<<<<<<....>>>.>>>>....}}..}}}.]]]]].....
<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<<<
....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>...>>>>...>>
>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>.>>
>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<<.<<<<
..>>>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<<
......>>>>>>>>>>>...>>>>..>>>..............>>>>..>
>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<....
.<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>
.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jdm Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Resolution: 2.67 Å
• Binding residue (original residue number in PDB): T2 K3 G4 T5 S6 S7 F8 G9 K10 R11 R12 N13 K14 T15 H16 K25 H28 Q30 K31 G35 K36 R43 K44 R45 K46 Y47 N48 W49 S50 K52 R55 R56 T58 T59 Y71 R75 K85
• Binding residue (residue number reindexed from 1): T1 K2 G3 T4 S5 S6 F7 G8 K9 R10 R11 N12 K13 T14 H15 K24 H27 Q29 K30 G34 K35 R42 K43 R44 K45 Y46 N47 W48 S49 K51 R54 R55 T57 T58 Y70 R74 K84

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding
• GO:0097371 MDM2/MDM4 family protein binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:1901798 positive regulation of signal transduction by p53 class mediator

Cellular Component

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

External links

• PDB: RCSB:8jdm, PDBe:8jdm, PDBj:8jdm
• PDBsum: 8jdm
• PubMed: 37992713
• UniProt: P61927|RL37_HUMAN Large ribosomal subunit protein eL37 (Gene Name=RPL37)