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Crystal structure of SARS-cov-2 main protease (mpro) variant K61A at 2.48 a resolution

Analyse Crystal structure of SARS-cov-2 main protease (mpro) variant K61A at 2.48 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZB8
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase NSP5
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	3C-like proteinase NSP5 (EC 3.4.22.69)	protein	306	21% helix, 28% strand	P0DTD1

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, C

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	1122	0.80	0.82	94	empty
2	218	0.63	0.82	33	DMS
3	390	0.56	0.74	46	DMS
4	214	0.47	0.74	27	empty
5	108	0.41	0.77	21	DMS

Interfaces

1 interface between chains.

A–C · 1527 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

7ZB8 · Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant K61A at 2.48 A resolution · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 7ZB8 · PDBe 7ZB8 · UniProt P0DTD1

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