Structure of PDB 8jdk Chain p Binding Site BS01

Receptor Information

>8jdk Chain p (length=69) Species: 9606 (Homo sapiens)

PRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKE
KAEKLKQSLPPGLAVKELK

Ligand information

>8jdk 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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>>>>>>..[[[..<<<<<...<<<<<<<<<<..>>>>>>.>>>>.....>
>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....<<<
<......>>>>.....((......<<<.....))>>>...>.>>>>>>>.
..>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>
>.....(((((..<<<<<<)))))..]]].....................
.............<<....>>...............<<<<....>>>>..
................................<<<<<<<<..<<<.<...
.<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<.<...<<<<.<<<<<
<.<<<...<..>.>>>>>>>>>.>>>>...>...>>>>>>>>>>>>>>>.
.....>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<.
.<<<.<<.<<<<......<<<<<<<....>>>>>>>.......>>>>.>>
>>>........>>>>>>..>>>>>>>>>>>....................
<<<<<..<<<<<<..>>>>>>.<<<<<<.<<<<.<<<<<<<<<<<.<<<<
<.<<<...<...........>....>>>.>>>>>.>.>>>>>>>.>>>..
.>>>>>>>>.>>..<<<<<<<..>>>>>.>>.....>>>>>.....>>>.
>>>>>....>>>>...>>>>>>>>..<<<<........>>>><<<<<<..
..<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>>>...
<<....>>...<<<<<<<<....>>>>>>>>..<<<<<...<<<..<<<.
.((((.((((>>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>
>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<
<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<.
.<<.<<........>>>>.>>>....>>>>>>>>>...<<.......>>.
.....>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.
<<<<<<<....................<<<.<<<<<<<<<...<<<....
<<<..<.<<<<...<<<<....>>>>.>>>>.>..>>>..>.>>...>>>
>>>>...<<<<<<<<<.........>>>>>>>>>....>>>>>>>>>>>>
..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...
<<<<<<<...<<<(((.......<<<<<.....<<..........<<<.<
<<<<<<<<<............>>>>>>>>>>>>>..........))).>>
...>>>>>..>>>...>>>>>>><<<<<<.<<<..........)))).))
))...............>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<
......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>
>>>><<.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<
<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<.
...<<<....>>>..........<<.<<<<<...........>>>>>>>.
.....>>....>>>..<<<<<........>>>>>))<<<<....<<<<<.
.<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<<<<<<...<
<<<<<<<<<<<.<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.
<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<
<<.......>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>
>..>..........>>.>>>.>>>>.>>>..>>.....<<......>>>>
>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<<.<<.....
....<.....<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<..
>>>>..>>>>>>.>>............<<<<<<<<<..<<<.........
>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<
<<..<<<<<<....<<<...<.<<<<....>>>>.>...>>>.>>>>..>
>>>><<<<<<.......>>>>>>........<...........<<<<<..
.....>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>
>>..>>>>>>....>>....<<<<<........>>>>>....[[[[[..{
{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<<.
.>>>>>>>>>...<<<<<.....<<<<......<..>.............
....<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>....>>
>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>
>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(
((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>><<<<...
.>>>>>>)))]......((((((..(((..>>>>>>.)))))))))....
......]]]]..}}]]]].......<<.<.<.<<<<<<...<<.......
>>...>>>>>>...>>.>.>........<<<<.<<<<<<..<.<.<<<<<
......>>>>>...>.>.<<<.........>>>.....>>>>>..>...>
>>.>.....<<<<<<<....>>>.>>>>....}}..}}}.]]]]].....
<<<<<<.<..<<<..<.<<<<<.................>>>>>.><<<<
....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>...>>>>...>>
>><<<<....<<<<<...........>>>>>....>>>>.>>>...>.>>
>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<<.<<<<
..>>>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<<
......>>>>>>>>>>>...>>>>..>>>..............>>>>..>
>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<....
.<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>
.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jdk Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Resolution: 2.26 Å
• Binding residue (original residue number in PDB): P2 R3 R17 D19 K24 K26 K33 K35 R37 S39 R40 Y41 L42 T44 L69 K70
• Binding residue (residue number reindexed from 1): P1 R2 R16 D18 K23 K25 K32 K34 R36 S38 R39 Y40 L41 T43 L68 K69

Gene Ontology

Molecular Function

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

Biological Process

• GO:0001501 skeletal system development
• GO:0001503 ossification
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0007605 sensory perception of sound
• GO:0022618 protein-RNA complex assembly
• GO:0034463 90S preribosome assembly
• GO:0042474 middle ear morphogenesis
• GO:0048318 axial mesoderm development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0033291 eukaryotic 80S initiation complex
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdk, PDBe:8jdk, PDBj:8jdk
• PDBsum: 8jdk
• PubMed: 37992713
• UniProt: P63173|RL38_HUMAN Large ribosomal subunit protein eL38 (Gene Name=RPL38)