Structure of PDB 7k5i Chain G Binding Site BS01

Receptor Information

>7k5i Chain G (length=230) Species: 9606 (Homo sapiens)

MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVV
RISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGC
IVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKE
DDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTK
KNKEEAAEYAKLLAKRMKEAKEKRQEQIAK

Ligand information

>7k5i Chain 2 (length=1665)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucucucucggccgaagcguuuacuuugaaaaaauuagagug
uucaaagcaggccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgaccggucggcguaa
cuucuuagagggacaaguggcguucagccacccgagauugagcaauaaca
ggucugugaugcccuuagauguccggggcugcacgcgcgcuacacugacu
ggcucagcguguccuacgccggcaggcgcggguaacccguugaaccccau
ucgugauggggaucggggauugcaauuauuccccaugaacgaggaauucc
caguaagugcgggucauaagcuugcguugauuaagucccugcccuuugua
cacaccgcccgucgcuacuaccgauuggaugguuuagugaggcccucgga
ucggccccgccggggugcccuggcggagcgcugagaagacggucgaacuu
gacuaucuagaggaaguaaaagucguaacaagguuuccguaggugaaccu
gcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7k5i SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): N4 P8 Q13 L15 S53 N56 K58 Q59 G60 Q65 G66 R72 L76 C83 Y84 R87 R88 G90 R92 R94 S96 V108 N110 R131 R132 L133 G134 P135 K136 R137 S139 R140 R154 Q155 R159 K160 L162 N163 K164 K167 R170 K172 A173 P174 K175 I176 Q177 R178 V180 R183 L185 Q186 H187 K188 R189 R190 R191 K195 K196 R198 K201
• Binding residue (residue number reindexed from 1): N4 P8 Q13 L15 S53 N56 K58 Q59 G60 Q65 G66 R72 L76 C83 Y84 R87 R88 G90 R92 R94 S96 V108 N110 R131 R132 L133 G134 P135 K136 R137 S139 R140 R154 Q155 R159 K160 L162 N163 K164 K167 R170 K172 A173 P174 K175 I176 Q177 R178 V180 R183 L185 Q186 H187 K188 R189 R190 R191 K195 K196 R198 K201

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

External links

• PDB: RCSB:7k5i, PDBe:7k5i, PDBj:7k5i
• PDBsum: 7k5i
• PubMed: 32995777
• UniProt: P62753|RS6_HUMAN Small ribosomal subunit protein eS6 (Gene Name=RPS6)