Research workbench

Crystal structure of the SARS-cov-2 main protease with a zinc ion coordinated in the active site

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

PDB: 7NTW
Type: protein
Length: 305 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: P0DTC1
Ligands: NA, ZN
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	3C-like proteinase (EC 3.4.22.69)	protein	305	26% helix, 29% strand	P0DTC1

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A
ZN · Zinc ion · metal · chains A
FMT · Formic acid · additive · 5 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.50	0.83	16	DMS
2	186	0.47	0.75	25	FMT, ZN
3	83	0.37	0.76	17	FMT

Compared structures

7NTW · Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the… · 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 7NTW · PDBe 7NTW · UniProt P0DTC1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.