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Crystal structure of a novel viral protease with a SERINE/LYSINE catalytic dyad mechanism

Analyse Crystal structure of a novel viral protease with a SERINE/LYSINE catalytic dyad… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GEF
Type: protein
Length: 401 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease VP4
EC: 3.4.21.-
UniProt: Q8AZM0
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease VP4 (EC 3.4.21.-)	protein	198	18% helix, 41% strand	Q8AZM0
B	Protease VP4 (EC 3.4.21.-)	protein	203	17% helix, 39% strand	Q8AZM0

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.65	0.80	51	empty
2	56	0.50	0.86	16	empty
3	62	0.46	0.84	19	empty

Interfaces

1 interface between chains.

A–B · 1532 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

2GEF · Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism · 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 Q8AZM0
Elsewhere: RCSB PDB 2GEF · PDBe 2GEF · UniProt Q8AZM0

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