Research workbench

The 1.28A crystal structure of 3CL mainpro of SARS-cov-2 with oxidized C145 (sulfinic acid cysteine)

Analyse The 1.28A crystal structure of 3CL mainpro of SARS-cov-2 with oxidized C145… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XKH
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	306	26% helix, 28% strand	P0DTD1

Ligands and binding sites

FMT · Formic acid · additive · 4 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.45	0.75	27	EDO, FMT
2	73	0.33	0.75	16	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

6XKH · THE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXIDIZED C145 (sulfinic… · 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 6XKH · PDBe 6XKH · UniProt P0DTD1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.