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Crystal structure of the SARS-cov-2 main protease

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

PDB: 7NTT
Type: protein
Length: 612 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: P0DTC1
Ligands: NA
Pockets: 6 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3C-like proteinase (EC 3.4.22.69)	protein	306	26% helix, 29% strand	P0DTC1

Ligands and binding sites

NA · Sodium ion · metal · chains A, B
FMT · Formic acid · additive · 2 copies · chains B

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

Pockets

6 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	947	0.76	0.79	79	empty
2	406	0.61	0.76	49	empty
3	220	0.52	0.77	29	empty
4	191	0.48	0.75	31	empty
5	203	0.47	0.75	31	empty

Interfaces

1 interface between chains.

A–B · 1654 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

7NTT · Crystal structure of the SARS-CoV-2 Main Protease · 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 P0DTC1
Elsewhere: RCSB PDB 7NTT · PDBe 7NTT · UniProt P0DTC1

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