Structure of PDB 8pyw Chain B

Receptor sequence
>8pywB (length=152) Species: 9606 (Homo sapiens) [Search protein sequence]
GANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQ
HYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSK
PGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEELVDYKSCAHDWV
YE
3D structure
PDB8pyw An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex.
ChainB
Resolution1.553 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.13.3: histidine kinase.
2.7.4.6: nucleoside-diphosphate kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 IF9 B L59 R62 F64 T98 V116 L55 R58 F60 T94 V112
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0004673 protein histidine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019003 GDP binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0051880 G-quadruplex DNA binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0007155 cell adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
GO:0018106 peptidyl-histidine phosphorylation
GO:0042981 regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0045618 positive regulation of keratinocyte differentiation
GO:0045682 regulation of epidermis development
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050679 positive regulation of epithelial cell proliferation
Cellular Component
GO:0001726 ruffle
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0030027 lamellipodium
GO:0034774 secretory granule lumen
GO:0042995 cell projection
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8pyw, PDBe:8pyw, PDBj:8pyw
PDBsum8pyw
PubMed38096103
UniProtP22392|NDKB_HUMAN Nucleoside diphosphate kinase B (Gene Name=NME2)

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