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The crystal structure of SARS-cov-2 main protease with the formation of CYS145-1H-indole-5-carboxylate

Analyse The crystal structure of SARS-cov-2 main protease with the formation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KYU
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: XC4
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	302	25% helix, 29% strand	P0DTD1

Ligands and binding sites

XC4 · 1-[(1H-indole-5-carbonyl)oxy]-1H-benzotriazole · ligand · chains A
EDO · 1,2-ethanediol · 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	188	0.48	0.76	25	XC4, EDO
2	72	0.33	0.75	14	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7KYU · The crystal structure of SARS-CoV-2 Main Protease with the formation of… · 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 7KYU · PDBe 7KYU · UniProt P0DTD1

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