Structure of PDB 8jdl Chain AF Binding Site BS01

Receptor Information

>8jdl Chain AF (length=143) Species: 9606 (Homo sapiens)

MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDE
NWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVA
RRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK

Ligand information

>8jdl 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: 8jdl Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Resolution: 2.42 Å
• Binding residue (original residue number in PDB): M1 G3 Q11 Q12 W33 K38 K43 E44 L45 Y48 R56 S59 R62 R67 G71 V72 G73 S74 K77 I78 R82 R84 G86 V87 M88 P89 H91 F92 S96 K97 S98 R101 Q105 K115 G120 R121 P125 Q128 R129 R133
• Binding residue (residue number reindexed from 1): M1 G3 Q11 Q12 W33 K38 K43 E44 L45 Y48 R56 S59 R62 R67 G71 V72 G73 S74 K77 I78 R82 R84 G86 V87 M88 P89 H91 F92 S96 K97 S98 R101 Q105 K115 G120 R121 P125 Q128 R129 R133

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0017134 fibroblast growth factor binding
• GO:0019901 protein kinase binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0002548 monocyte chemotaxis
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0007000 nucleolus organization
• GO:0030218 erythrocyte differentiation
• GO:0030490 maturation of SSU-rRNA
• GO:0031640 killing of cells of another organism
• GO:0042274 ribosomal small subunit biogenesis
• GO:0050829 defense response to Gram-negative bacterium
• GO:0060265 positive regulation of respiratory burst involved in inflammatory response
• GO:0060266 negative regulation of respiratory burst involved in inflammatory response
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

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:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdl, PDBe:8jdl, PDBj:8jdl
• PDBsum: 8jdl
• PubMed: 37992713
• UniProt: P39019|RS19_HUMAN Small ribosomal subunit protein eS19 (Gene Name=RPS19)