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SARS-cov-2 main protease in orthorhombic space group

Analyse SARS-cov-2 main protease in orthorhombic space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MBG
Type: protein
Length: 604 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 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
B	3C-like proteinase (EC 3.4.22.69)	protein	302	24% helix, 29% strand	P0DTD1

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · 14 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1039	0.76	0.79	96	DMS
2	162	0.56	0.81	35	DMS
3	220	0.51	0.76	34	empty
4	255	0.48	0.73	48	DMS
5	219	0.48	0.75	32	DMS

Interfaces

1 interface between chains.

A–B · 1501 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

7MBG · SARS-CoV-2 Main protease in orthorhombic space group · 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 7MBG · PDBe 7MBG · UniProt P0DTD1

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