PDBsum entry 8s8w

Viral protein

PDB id: 8s8w

Contents

Protein chains

299 a.a.

114 a.a.

DNA/RNA

Ligands

MES

SAM

SGV

EDO ×3

GTA

Metals

_ZN ×2

Waters ×183

PDB id:

8s8w

Name:

Viral protein

Title:

Sars-cov-2 nsp10-16 methyltransferase in complex with sangivamycin and m7gpppa-RNA (cap0-RNA)

Structure:

2'-o-methyltransferase nsp16. Chain: a. Synonym: non-structural protein 16,nsp16. Engineered: yes. Non-structural protein 10. Chain: b. Synonym: nsp10,growth factor-like peptide,gfl. Engineered: yes. M7gpppa-RNA (cap0-RNA).

Source:

Severe acute respiratory syndrome coronavirus 2. Organism_taxid: 2697049. Gene: rep, 1a-1b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.10Å R-factor: 0.188 R-free: 0.224

Authors:

V.Kremling,J.Sprenger,D.Oberthuer,T.E.S.Scheer

Key ref:

V.Kremling et al. Sars-Cov-2 methyltransferase nsp10-16 in complex with natural and drug-Like purine analogs for guiding structure-Based drug development. To be published, .

Date:

07-Mar-24 Release date: 20-Mar-24

Protein chain

P0DTD1  (R1AB_SARS2) -

Protein chain

P0DTD1  (R1AB_SARS2) -

DNA/RNA chain

U-U-A 3 bases

Enzyme reactions

• Enzyme class: Chain A: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site