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Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Boceprevir

Analyse Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XQU
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: U5G
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · resolution 2.2 · 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	306	25% helix, 29% strand	P0DTD1

Ligands and binding sites

U5G · boceprevir (bound form) · ligand · 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	200	0.48	0.75	31	U5G
2	144	0.42	0.75	28	empty

Modifications

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

Compared structures

6XQU · Room-temperature X-ray crystal structure of SARS-cov-2 main protease in complex with… · 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 6XQU · PDBe 6XQU · UniProt P0DTD1

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