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Crystal structure of SARS-cov-2 main protease (mpro) H172Y mutant in complex with inhibitor GC376

Analyse Crystal structure of SARS-cov-2 main protease (mpro) H172Y mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8D4K
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase NSP5
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: K36
Pockets: 3 · best druggability 0.53

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase NSP5 (EC 3.4.22.69)	protein	304	26% helix, 29% strand	P0DTD1

Ligands and binding sites

K36 · (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 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	170	0.53	0.79	28	K36
2	52	0.46	0.85	17	empty
3	74	0.32	0.74	18	empty

Modifications

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

Compared structures

8D4K · Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant in Complex with… · 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 8D4K · PDBe 8D4K · UniProt P0DTD1

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