MolNFT v1 · #132921 · protein

Pandda analysis group deposition -- crystal structure of SARS-cov-2 main protease in complex with pcm-0102911

5REY · 3C-like proteinase: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 main protease in complex with pcm-0102911”. X-ray diffraction, 1 ligand (T4Y), 4 pockets (best druggability 0.54). MolNFT v1 #132921 on…

PDB: 5REY
Type: protein
Length: 304 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: P0DTD1
Ligands: T4Y
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	304	24% helix, 29% strand	P0DTD1

Ligands and binding sites

T4Y · 1-{4-[(2-methylphenyl)methyl]-1,4-diazepan-1-yl}ethan-1-one · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.54	0.77	26	T4Y
2	89	0.48	0.82	21	DMS
3	62	0.35	0.77	15	empty
4	67	0.29	0.74	14	empty

Modifications

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

Compared structures

5REY · 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 5REY · PDBe 5REY · UniProt P0DTD1

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