Structure of PDB 7k0r Chain F Binding Site BS02

Receptor Information

>7k0r Chain F (length=345) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

MSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTL
PVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTI
GVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVK
GLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRN
LQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLH
LLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLL
DDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPK

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 7k0r Chain F Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7k0r Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): H235 G247 G248 K290 T341
• Binding residue (residue number reindexed from 1): H235 G247 G248 K290 T341
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

External links

• PDB: RCSB:7k0r, PDBe:7k0r, PDBj:7k0r
• PDBsum: 7k0r
• PubMed: 33504779
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)