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Structure of SARS-cov-2 main protease bound to thioglucose.

Analyse Structure of SARS-cov-2 main protease bound to thioglucose. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ARF
Type: protein
Length: 302 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
Ligands: RVW, CL
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	302	26% helix, 29% strand	P0DTD1

Ligands and binding sites

RVW · (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol · ligand · chains A
CL · Chloride ion · ion · chains A
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

3 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	57	0.46	0.84	13	DMS
2	158	0.44	0.75	24	empty
3	81	0.33	0.74	16	empty

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, oxidation).

Compared structures

7ARF · Structure of SARS-CoV-2 Main Protease bound to thioglucose. · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 7ARF · PDBe 7ARF · UniProt P0DTD1

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