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Crystal structure of a lanthipeptide protease

Analyse Crystal structure of a lanthipeptide protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZOQ
Type: protein
Length: 3,174 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Intracellular serine protease
UniProt: Q65DC7
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Intracellular serine protease	protein	61	38% helix, 31% strand	Q65DC7
I, J, L, P	Intracellular serine protease	protein	337	37% helix, 19% strand	Q65DC7
B, C, D	Intracellular serine protease	protein	60	35% helix, 30% strand	Q65DC7
K, N, O	Intracellular serine protease	protein	335	36% helix, 18% strand	Q65DC7
M	Intracellular serine protease	protein	333	35% helix, 20% strand	Q65DC7
F, G, H	Intracellular serine protease	protein	62	24% helix, 31% strand	Q65DC7

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.81	0.82	102	empty
2	853	0.75	0.79	87	empty
3	683	0.74	0.81	64	empty
4	1022	0.74	0.77	82	empty
5	150	0.68	0.88	29	empty

Interfaces

27 interfaces between chains.

I–L · 1041 Å² buried · 18 hydrogen bonds · protein-protein
O–P · 759 Å² buried · 3 hydrogen bonds · protein-protein
A–I · 742 Å² buried · 11 hydrogen bonds · protein-protein
C–K · 740 Å² buried · 9 hydrogen bonds · protein-protein
D–L · 737 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4ZOQ · Crystal Structure of a Lanthipeptide Protease · 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 Q65DC7
Elsewhere: RCSB PDB 4ZOQ · PDBe 4ZOQ · UniProt Q65DC7

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