Structure of PDB 7diy Chain B Binding Site BS01

Receptor Information

>7diy Chain B (length=286) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

NVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYR
RLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVG
TNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPL
MYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIG
PERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGN
LQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVK

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 7diy Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7diy Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity.
• Resolution: 2.693 Å
• Binding residue (original residue number in PDB): C207 C210 C226 H229
• Binding residue (residue number reindexed from 1): C205 C208 C224 H227
• 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.-

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0004532 RNA exonuclease activity
• GO:0008168 methyltransferase activity

External links

• PDB: RCSB:7diy, PDBe:7diy, PDBj:7diy
• PDBsum: 7diy
• PubMed: 33956156
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)