Structure of PDB 8jdl Chain z Binding Site BS01

Receptor Information
>8jdl Chain z (length=212) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLK
IMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAP
VPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKE
TVFTKSPYQEFT
Ligand information
>8jdl Chain w (length=1634) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8jdl Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
Resolution2.42 Å
Binding residue
(original residue number in PDB)		V112 Q113 K114 Q115 R117 Q120 K125 T185 R187 G189 S190 R194 V205 S206 Y223 T224 A226 R227 C229 T230 T232 N235
Binding residue
(residue number reindexed from 1)		V54 Q55 K56 Q57 R59 Q62 K67 T127 R129 G131 S132 R136 V147 S148 Y165 T166 A168 R169 C171 T172 T174 N177
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0017134 fibroblast growth factor binding
GO:0019899 enzyme binding
GO:0045296 cadherin binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0051443 positive regulation of ubiquitin-protein transferase activity
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:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8jdl, PDBe:8jdl, PDBj:8jdl
PDBsum8jdl
PubMed37992713
UniProtP15880|RS2_HUMAN Small ribosomal subunit protein uS5 (Gene Name=RPS2)

[Back to BioLiP]