Structure of PDB 8glp Chain SB Binding Site BS01

Receptor Information

>8glp Chain SB (length=223) Species: 9606 (Homo sapiens)

AVGKNKRLTVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDG
LKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMC
SMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQV
RQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVF
VRKVKMLKKPKFELGKLMELHGE

Ligand information

>8glp Chain S2 (length=1672)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgccacuuggauaacuguggua
auucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggg
augcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcac
gccccccguggcggcgacgacccauucgaacgucugcccuaucaacuuuc
gaugguagucgccgugccuaccauggugaccacgggugacggggaaucag
gguucgauuccggagagggagccugagaaacggcuaccacauccaaggaa
ggcagcaggcgcgcaaauuacccacucccgacccggggagguagugacga
aaaauaacaauacaggacucuuucgaggcccuguaauuggaaugagucca
cuuuaaauccuuuaacgaggauccauuggagggcaagucuggugccagca
gccgcgguaauuccagcuccaauagcguauauuaaaguugcugcaguuaa
aaagcucguaguuggaucuuuuuacuuugaaaaaauuagaguguucaaag
caggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccg
cgguucuauuuuguugguuuucggaacugaggccaugauuaagagggacg
gccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcg
caagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaa
gaacgaaagucggagguucgaagacgaucagauaccgucguaguuccgac
cauaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgcc
gggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguu
gcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugga
gccugcggcuuaauuugacucaacacgggaaaccucacccggcccggaca
cggacaggauugacagauugauagcucuuucucgauuccguggguggugg
ugcauggccguucuuaguugguggagcgauuugucugguuaauuccgaua
acgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucg
gcgucccccaacuucuuagagggacaaguggcguucagccacccgagauu
gagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcg
cuacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggu
aacccguugaaccccauucgugauggggaucggggauugcaauuauuccc
caugaacgaggaauucccaguaagugcgggucauaagcuugcguugauua
agucccugcccuuuguacacaccgcccgucgcuacuaccgauuggauggu
uuagugaggcccucggaucggccccgccggcggagcgcugagaagacggu
cgaacuugacuaucuagaggaaguaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8glp mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): V3 K5 N6 K7 R8 T10 P24 K28 K56 S112 V114 K115 K116 W117 Q118 M120 H124 R136 F138 R146 N148 Q149 I150 R151 Y155 Q157 H158 Q159 Q160 R162 R165 Q202 S203 I204 Y205 P206 K214 K216
• Binding residue (residue number reindexed from 1): V2 K4 N5 K6 R7 T9 P13 K17 K45 S101 V103 K104 K105 W106 Q107 M109 H113 R125 F127 R135 N137 Q138 I139 R140 Y144 Q146 H147 Q148 Q149 R151 R154 Q191 S192 I193 Y194 P195 K203 K205

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0030154 cell differentiation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0043066 negative regulation of apoptotic process

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8glp, PDBe:8glp, PDBj:8glp
• PDBsum: 8glp
• PubMed: 37020024
• UniProt: P61247|RS3A_HUMAN Small ribosomal subunit protein eS1 (Gene Name=RPS3A)