Structure of PDB 8ppl Chain AG Binding Site BS01

Receptor Information
>8ppl Chain AG (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVV
RISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGC
IVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKE
DDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTK
KNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
Ligand information
>8ppl Chain A2 (length=1780) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucagaucaaaaccaacccggugccggcggcuuugguga
cucuagauaaccucgggccgaucgcacgccccccguggcggcgacgaccc
auucgaacgucugcccuaucaacuuucgaugguagucgccgugccuacca
uggugaccacgggugacggggaaucaggguucgauuccggagagggagcc
ugagaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuaccc
acucccgacccggggagguagugacgaaaaauaacaauacaggacucuuu
cgaggcccuguaauuggaaugaguccacuuuaaauccuuuaacgaggauc
cauuggagggcaagucuggugccagcagccgcgguaauuccagcuccaau
agcguauauuaaaguugcugcaguuaaaaagcucguaguuggaucuuggg
agcgggcgggcgguaccgcccguccccgcccgccucucggcgccccgggg
cccgaagcguuuacuuugaaaaaauuagaguguucaaagcaggcccgagc
cgccuggauaccgcagcuaggaauaauggaauaggaccgcgguucuauuu
uguugguuuucggaacugaggccaugauuaagagggacggccgggggcau
ucguauugcgccgcuagaggugaaauucuuggaccggcgcaagacggacc
agagcgaaagcauuugccaagaauguuuucauuaaucaagaacgaaaguc
ggagguucgaagacgaucagauaccgucguaguuccgaccauaaacgaug
ccgaccggcgaugcggcggcguuauucccaugacccgccgggcagcuucc
gggaaaccaaagucuuuggguuccggggggaguaugguugcaaagcugaa
acuuaaaggaauugacggaagggcaccaccaggaguggagccugcggcuu
aauuugacucaacacgggaaaccucacccggcccggacacggacaggauu
gacagauugauagcucuuucucgauuccgugggugguggugcauggccgu
ucuuaguugguggagcgauuugucugguuaauuccgauaacgaacgagac
ucuggcaugcuaacuaguuacgcgacccccgagcggucggcgucccccaa
cuucuuagagggacaaguggcguucagccacccgagauugagcaauaaca
ggucugugaugcccuuagauguccggggcugcacgcgcgcuacacugacu
ggcucagcgugugccuacccuacgccggcaggcgcggguaacccguugaa
ccccauucgugauggggaucggggauugcaauuauuccccaugaacgagg
aauucccaguaagugcgggucauaagcuugcguugauuaagucccugccc
uuuguacacaccgcccgucgcuacuaccgauuggaugguuuagugaggcc
cucggaucggccccgccggggucggcccacggcccuggcggagcgcugag
aagacggucgaacuugacuaucuagaggaaguaaaagucguaacaagguu
uccguaggugaaccugcggaaggaucauua
...<<<<<...[[[[>>>>>[[[.((((((.....{{.........[[[.
[[[..<<....<<....<<..........>>...>>.>>......{{...
.....[[[......{{....[[[{..........<<.....<<.<<<...
..>>>.>>......>>.........<<<<...<<<<<<....>>>>>>..
.>>>>[[..(((((.....<<<<<<<<<<<<<..>>>>.......<....
..>..)))))......]]...<<<<.<<<<......>>>>>>>>..}.]]
]...}}....]]].<<<....<<<....<<<<<<<.........>>>>>>
>>>>......>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.
.........>>>.>>.<.<<....>>.>...]]]]]].........<<<.
...<<<<...>>>>..>>>......}}.......<<<<<<<<<.<<<...
.>>>..>>>>>>.>>>......<<..<...........>..>>.......
..<<<<<((......<<<<.....<<..))>>.......>>>>.>>>>>.
.)))))).]]]............{{.......{{...[[[.[[....<<<
.<.<<<<<<<<<<..>>>>>>>>>>.>.>>><<...<<<..<<<<<>>>>
>.>>>.>>..<<<<<<.<.......<<...<.......>.<<<<......
.>>>>...>>......>.>>>..>>>........{.[[.(((((((....
.>>>>>>>>>.))))))).]].}....]]....<<<<<<..<...<<<<.
.<<..<<<<<<<<...<<<......>>>......>>>>>>>>..>>....
...<<....>>...>>>>..>..>>>.>>>...]]]...}}......<<<
<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>..........<
<<.<<.<<<..<.<<<<<<.<<<........>>>>>>>>>.>..>>>...
<<..}}>>...>>.....>>>.....<<<......<<<......>>>...
.>>>..]]]]..<<<<<.<<<<<<<..<<..<<<<<..<<<.<<<<<<..
....<<........>>..........<<<<<......<<<<<<.......
<<.<<<........>>>.>>.....>>>>>>...<<.<<<..<<.<<<<<
<....<<<.<<<<<....>>>...<<<......>>>...>>.>>>....<
<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>>>>.....>>
>>..>>>>..>.....<<<<<.....>>>>>........>>>....>>>.
>>>.....>>>>>>>.......>>>>>...>>.>>>>.>>>.....<<.<
<<........<.......<<<.<<<<....>>>>.>>>....>.......
..>>>.>>............<<<<<..........>>>>>..........
.>>>>>.....<<<<<<<<.......>>>>>>>>......>>...>>>>>
>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<<<..<<<<
.<<...<<<<<.<<<<<<<<<<<<.....>>>>>>>>>>>>...>>>>>.
..>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<
<<<<<<<<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ppl Universal features of Nsp1-mediated translational shutdown by coronaviruses.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		N4 P8 G11 Q13 L15 R31 S53 K58 Q59 G60 F61 Q65 G66 R72 L75 L76 C83 Y84 R87 R88 T89 G90 R92 K93 R94 K95 S96 S107 V108 N110 R132 L133 G134 K136 R137 S139 R140 K143 R154 Q155 R159 K160 L162 K164 K167 K168 R170 K172 A173 P174 K175 I176 R178 V180 R183 V184 Q186 H187 K188 R189 R190 R191 I192 K195 K196 R198 T199 K201 K221 R224 R231 R232 R233 L234 L237
Binding residue
(residue number reindexed from 1)		N4 P8 G11 Q13 L15 R31 S53 K58 Q59 G60 F61 Q65 G66 R72 L75 L76 C83 Y84 R87 R88 T89 G90 R92 K93 R94 K95 S96 S107 V108 N110 R132 L133 G134 K136 R137 S139 R140 K143 R154 Q155 R159 K160 L162 K164 K167 K168 R170 K172 A173 P174 K175 I176 R178 V180 R183 V184 Q186 H187 K188 R189 R190 R191 I192 K195 K196 R198 T199 K201 K221 R224 R231 R232 R233 L234 L237
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019901 protein kinase binding
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000278 mitotic cell cycle
GO:0001890 placenta development
GO:0002181 cytoplasmic translation
GO:0002309 T cell proliferation involved in immune response
GO:0006364 rRNA processing
GO:0006412 translation
GO:0006924 activation-induced cell death of T cells
GO:0007369 gastrulation
GO:0008284 positive regulation of cell population proliferation
GO:0022605 mammalian oogenesis stage
GO:0031929 TOR signaling
GO:0033077 T cell differentiation in thymus
GO:0042274 ribosomal small subunit biogenesis
GO:0042593 glucose homeostasis
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0048821 erythrocyte development
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:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0030425 dendrite
GO:0032040 small-subunit processome
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0044297 cell body
GO:0048471 perinuclear region of cytoplasm
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ppl, PDBe:8ppl, PDBj:8ppl
PDBsum8ppl
PubMed37802027
UniProtP62753|RS6_HUMAN Small ribosomal subunit protein eS6 (Gene Name=RPS6)

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