Structure of PDB 6wkq Chain D Binding Site BS02

Receptor Information

>6wkq Chain D (length=116) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

AFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES
FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVC
TVCGMWKGYGCSCDQL

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: 6wkq Chain D Residue 4402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wkq High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): C4370 C4373 C4381 C4383
• Binding residue (residue number reindexed from 1): C100 C103 C111 C113
• 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:0003723 RNA binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0019079 viral genome replication

External links

• PDB: RCSB:6wkq, PDBe:6wkq, PDBj:6wkq
• PDBsum: 6wkq
• PubMed: 32994211
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)