Structure of PDB 6zme Chain SD Binding Site BS02

Receptor Information
>6zme Chain SD (length=227) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIII
LATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIA
QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSM
KFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGP
KKPLPDHVSIVEPKDEILPTTPISEQK
Ligand information
>6zme Chain CF (length=29) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
DPYEDFQENWNTKHSSGVTRELMRELNGG
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6zme Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		A114 R116 R143 K148 M150
Binding residue
(residue number reindexed from 1)		A114 R116 R143 K148 M150
Enzymatic activity
Enzyme Commision number 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0004520 DNA endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0015631 tubulin binding
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0019899 enzyme binding
GO:0019900 kinase binding
GO:0019901 protein kinase binding
GO:0030544 Hsp70 protein binding
GO:0032357 oxidized purine DNA binding
GO:0032358 oxidized pyrimidine DNA binding
GO:0044390 ubiquitin-like protein conjugating enzyme binding
GO:0044877 protein-containing complex binding
GO:0051018 protein kinase A binding
GO:0051536 iron-sulfur cluster binding
GO:0051879 Hsp90 protein binding
GO:0070181 small ribosomal subunit rRNA binding
GO:0097100 supercoiled DNA binding
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0140297 DNA-binding transcription factor binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006412 translation
GO:0006413 translational initiation
GO:0006417 regulation of translation
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007059 chromosome segregation
GO:0010628 positive regulation of gene expression
GO:0017148 negative regulation of translation
GO:0031116 positive regulation of microtubule polymerization
GO:0031334 positive regulation of protein-containing complex assembly
GO:0031397 negative regulation of protein ubiquitination
GO:0032079 positive regulation of endodeoxyribonuclease activity
GO:0032743 positive regulation of interleukin-2 production
GO:0034614 cellular response to reactive oxygen species
GO:0042104 positive regulation of activated T cell proliferation
GO:0042981 regulation of apoptotic process
GO:0043507 positive regulation of JUN kinase activity
GO:0045738 negative regulation of DNA repair
GO:0045739 positive regulation of DNA repair
GO:0050862 positive regulation of T cell receptor signaling pathway
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0051225 spindle assembly
GO:0051301 cell division
GO:0061481 response to TNF agonist
GO:0070301 cellular response to hydrogen peroxide
GO:0071356 cellular response to tumor necrosis factor
GO:1901224 positive regulation of non-canonical NF-kappaB signal transduction
GO:1902231 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1905053 positive regulation of base-excision repair
GO:2001235 positive regulation of apoptotic signaling pathway
GO:2001272 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005783 endoplasmic reticulum
GO:0005819 spindle
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0014069 postsynaptic density
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032587 ruffle membrane
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0071159 NF-kappaB complex
GO:0072686 mitotic spindle
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6zme, PDBe:6zme, PDBj:6zme
PDBsum6zme
PubMed32680882
UniProtP23396|RS3_HUMAN Small ribosomal subunit protein uS3 (Gene Name=RPS3)

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