Structure of SARS-cov-2 NSP16/NSP10 complex in presence of cap-1 analog (M7GPPPAMU) and sah

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 19% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · chains A
• YG4 · [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R}, 3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains B
• MG · Magnesium ion · metal · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
• EDO · 1,2-ethanediol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 861 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7LW3 · Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of Cap-1 analog (m7GpppAmU) and… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P0DTD1
• Elsewhere: RCSB PDB 7LW3 · PDBe 7LW3 · UniProt P0DTD1