Structure of PDB 8jdk Chain g Binding Site BS01

Receptor Information

>8jdk Chain g (length=104) Species: 9606 (Homo sapiens)

AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNK
KGLKKMQANNAKAMSARAEAIKALVVSRKLDRLAYIAHPKLGKRARARIA
KGLR

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): A2 K3 S4 K5 N6 H7 T8 T9 H10 N11 Q12 S13 R14 K15 H17 R18 N19 S26 Q27 R28 Y29 L32 K33 D36 F39 R41 N42 R44 F45 A46 K47 K48 H49 N50 K52 K56 M57 N60 N61 S90 R91 K92 R95 Y98 H101 P102 A108 R111 K114 G115
• Binding residue (residue number reindexed from 1): A1 K2 S3 K4 N5 H6 T7 T8 H9 N10 Q11 S12 R13 K14 H16 R17 N18 S25 Q26 R27 Y28 L31 K32 D35 F38 R40 N41 R43 F44 A45 K46 K47 H48 N49 K51 K55 M56 N59 N60 S77 R78 K79 R82 Y85 H88 P89 A95 R98 K101 G102

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008201 heparin binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0007566 embryo implantation

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:8jdk, PDBe:8jdk, PDBj:8jdk
• PDBsum: 8jdk
• PubMed: 37992713
• UniProt: P47914|RL29_HUMAN Large ribosomal subunit protein eL29 (Gene Name=RPL29)