MolNFT v2 · #133332 · protein

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102275

5REW · 3C-like proteinase: “PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102275”. X-ray diffraction at 1.55, 1 ligand (T4M), 4 pockets (best druggability 0.48). MolNFT v2 #133332 on…

PDB: 5REW
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.55
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: T4M
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · resolution 1.55 · 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	304	26% helix, 29% strand	P0DTD1

Ligands and binding sites

T4M · N-[(1R)-1-(naphthalen-1-yl)ethyl]acetamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A

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

Pockets

4 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	95	0.48	0.81	19	DMS
2	183	0.48	0.76	25	T4M
3	58	0.32	0.76	16	empty
4	71	0.30	0.74	16	empty

Modifications

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

Compared structures

5REW · Pandda analysis group deposition -- crystal structure of SARS-cov-2 main protease in… · 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 5REW · PDBe 5REW · UniProt P0DTD1

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