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Crystal structure of the SARS-cov-2 main protease with oxidized C145

Analyse Crystal structure of the SARS-cov-2 main protease 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: 7NTS
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicase polyprotein 1AB
EC: 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt: P0DTD1
Pockets: 3 · best druggability 0.50

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replicase polyprotein 1AB (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)	protein	305	26% helix, 29% strand	P0DTD1

Ligands and binding sites

FMT · Formic acid · additive · 9 copies · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.50	0.86	15	DMS
2	160	0.46	0.76	25	FMT
3	145	0.42	0.75	27	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

7NTS · Crystal structure of the SARS-CoV-2 Main Protease with oxidized C145 · 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 7NTS · PDBe 7NTS · UniProt P0DTD1

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