MolNFT v1 · #177049 · protein

The crystal structure of COVID-19 main protease apo form at 2.2 ångström

7E5X · 3C-like proteinase: “The crystal structure of COVID-19 main protease apo form at 2.2 ångström”. X-ray diffraction, 15 pockets (best druggability 0.79). MolNFT v1 #177049 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7E5X
Type: protein
Length: 1,224 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 15 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	3C-like proteinase (EC 3.4.22.69)	protein	306	24% helix, 29% strand	P0DTD1

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	966	0.79	0.81	98	empty
2	769	0.78	0.82	74	empty
3	649	0.78	0.84	68	empty
4	169	0.66	0.86	29	empty
5	363	0.58	0.76	53	empty

Interfaces

5 interfaces between chains.

C–D · 1515 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1462 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 656 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 331 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 72 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7E5X · THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE apo form at 2.2 angstrom · 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 7E5X · PDBe 7E5X · UniProt P0DTD1

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