MolNFT v1 · #132978 · protein

Pandda analysis group deposition SARS-cov-2 main protease fragment screen -- crystal structure of SARS-cov-2 main protease in complex with Z1401276297 (mpro-X0425)

5RGJ · 3C-like proteinase: “Pandda analysis group deposition SARS-cov-2 main protease fragment screen -- crystal structure of SARS-cov-2…”. X-ray diffraction, 1 ligand (U0S), 4 pockets (best druggability 0.51). MolNFT v1 #132978 on…

PDB: 5RGJ
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: U0S
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 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

U0S · (5S)-7-(pyrazin-2-yl)-2-oxa-7-azaspiro[4.4]nonane · 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	208	0.51	0.77	24	empty
2	79	0.47	0.82	18	DMS
3	79	0.32	0.74	15	empty
4	55	0.31	0.76	17	empty

Compared structures

5RGJ · PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal… · 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 5RGJ · PDBe 5RGJ · UniProt P0DTD1

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