Structure of PDB 8jdk Chain 6 Binding Site BS01

Receptor Information

>8jdk Chain 6 (length=182) Species: 9606 (Homo sapiens)

PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLA
KIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLK
IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRL
DSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQG

Ligand information

>8jdk Chain w (length=1634)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacgacagugaaacugcgaauggcucauuaaauc
aguuaugguuccuuuggucgcucgacuuggauaacugugguaauucuaga
gcuaauacaugccgacgggcgcugacccccuucgcgggggggaugcgugc
auuuaucagauggugacucuagauaaccgccgaucgcacgcgcggcgacg
acccauucgaacgucugcccuaucaacuuucgaugguagucgccgugccu
accauggugaccacgggugacggggaaucaggguucgauuccggagaggg
agccugagaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauu
acccacucccgacccggggagguagugacgaaaaauaacaauacaggccc
uguaauuggaaugaguccacuuuaaauccuuccgcgaggauccauuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguaua
uuaaaguugcugcaguuaaaaagcucguaguuggaucuuuuacuuugaaa
aaauuagaguguucaaagcaggcccgagccgccuggauaccgcagcuagg
aauaauggaauaggaccgcgguucuauuuuguugguuuucggaacugagg
ccaugauuaagagggacggccgggggcauucguauugcgccgcuagaggu
gaaauucuuggaccggcgcaagacggaccagagcgaaagcauuugccaag
aauguuuucauuaaucaagaacgaaagucggagguucgaagacgaucaga
uaccgucguaguuccgaccauaaacgaugccgacuggcgaugcggcggcg
uuauucccaugacccgccgggcagcuuccgggaaaccaaagucuuugggu
uccggggggaguaugguugcaaagcugaaacuuaaaggaauugacggaag
ggcaccaccaggaguggagccugcggcuuaauuugacucaacacgggaaa
ccucacccggcccggacacggacaggauugacagauugauagcucuuucu
cgauuccgugggugguggugcauggccguucuuaguugguggagcgauuu
gucugguuaauuccgauaacgaacgagacucuggcaugcuaacuaguuac
gcgacccgcggucggcgucccccaacuucuuagagggacaaguggcguuc
agccacccgagauugagcaauaacaggucugugaugcccuuagauguccg
gggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacgc
cggcaggcgcggguaacccguugaaccccauucgugauggggaucgggga
uugcaauuauuccccaugaacgaggaauucccaguaagugcgggucauaa
gcuugcguugauuaagucccugcccuuuguacacaccgcccgucgcuacu
accgauuggaugguuuagugaggcccucggaucggccccgcgcggagcgc
ugagaagacggucgaacuugacuaucuagaggaaguaaaagucguaacaa
gguuuccguaggugaaccugcggaaggaucauua

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<....>>...>>.>>......<<........<
<<.<....<<....<<<<.........<<.....<<.<<<.....>>>.>
>......>>.........<<<<...<<<<<......>>>>>...>>>><<
..<<<<<....<......>..>>>>>..>>...<<<<.<<..>>>>>>..
>.>>>...>>..>.>>>.<<<....<<<....<<<<<<<.........>>
>>>>>>>>......>>>...<<<.<<<<....>>>>....>>>.>>.<<.
<<<..........>>>.>>.<.<<....>>.>...>>>>>>.........
<<<....<<.......>>..>>>..>...>>.>.....<<.<<<.<..>.
.>>>..>>......<<..<...........>..>>.........<<<<<(
(......<<<<.....<<..))>>.......>>>>.>>>>>..>>>>>>.
>>>.........<.<((.....<.<<...<<<.<<....<<<<<<.<...
....<<...<.......>.<<<<.......>>>>...>>......>.>>>
..>>>........<.<<.<<<<.<<...............>>.>>>>.>>
.>....>>....<<<<<<..<...<<<<..<<..<<<<<<<<...<<<..
....>>>......>>>>>>>>..>>.......<<....>>...>>>>..>
..>>>.>>>...>>>...>>.>....<<<<<<<...<...<<<<.<....
.>.>>>>...>>>>>>>>..........<<<.<<.<<<..<.<<<<<<.<
<<<......>>>>>>>>>>.>..>>>...<<..))>>...>>.....>>>
.>.>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<
<<<<..<<..<<<<<..<<<.<<<<<<......<<........>>.....
.....<<<<<.<....<<<<<<.......<<.<<<........>>>.>>.
....>>>>>>.<.<<.<<<..<<.<<<<<<....<<<.<<<<<....>>>
...<<<......>>>...>>.>>>....<<<...<...<<<<..<<<<<<
<<<<<<...>>>>.>>>>.....>>>>..>>>>..>.....<<<<<....
.>>>>>........>>>....>>>.>>>.....>>>>>>>>....>.>>>
>>...>>.>>>>.>>>.....<<.<<<........<.......<<<.<<<
<....>>>>.>>>....>.........>>>.>>......<.....<<<<<
..........>>>>>.....>.....>>>>>.....<<<<<<<<......
.>>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<..<<<<
.<<....<<<<<<<<.<<<..<<<<.<<...<<<<<...<..>.....>>
>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.>>...>..
...<<<<<<<<<<..>>>>>>>>>>.........

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 A4 R5 S6 W7 V8 R10 K11 Y13 T15 R17 R18 P19 F20 K22 R38 N39 K40 R41 R45 R69 F72 E73 R80 K121 S122 H124 H125 R131 Q132 H134 Q140 V142 I144 P145 S146 F147 I148 R150 R162 P164 Y165 R169 G171 V173 K174 R175 N177
• Binding residue (residue number reindexed from 1): P1 A3 R4 S5 W6 V7 R9 K10 Y12 T14 R16 R17 P18 F19 K21 R37 N38 K39 R40 R44 R68 F71 E72 R79 K120 S121 H123 H124 R130 Q131 H133 Q139 V141 I143 P144 S145 F146 I147 R149 R161 P163 Y164 R168 G170 V172 K173 R174 N176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0008284 positive regulation of cell population proliferation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0043226 organelle
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdk, PDBe:8jdk, PDBj:8jdk
• PDBsum: 8jdk
• PubMed: 37992713
• UniProt: P46781|RS9_HUMAN Small ribosomal subunit protein uS4 (Gene Name=RPS9)