MolNFT v1 · #82062 · protein

Crystal structure of SARS-cov 3C-like protease in apo form

3VB3 · 3C-like proteinase: “Crystal structure of SARS-cov 3C-like protease in apo form”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #82062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VB3
Type: protein
Length: 607 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.-
UniProt: P0C6U8
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.-)	protein	301	26% helix, 30% strand	P0C6U8
B	3C-like proteinase (EC 3.4.22.-)	protein	306	25% helix, 29% strand	P0C6U8

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 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	876	0.76	0.80	74	PEG, EDO
2	478	0.65	0.77	69	empty
3	62	0.61	0.91	24	empty
4	164	0.47	0.76	21	empty
5	181	0.45	0.75	28	empty

Interfaces

1 interface between chains.

A–B · 1415 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

3VB3 · Crystal structure of SARS-CoV 3C-like protease in apo form · the same entry in another collection · chain B against B, 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 P0C6U8
Elsewhere: RCSB PDB 3VB3 · PDBe 3VB3 · UniProt P0C6U8

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