Research workbench

Lon protease proteolytic domain

Analyse Lon protease proteolytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZV
Type: protein
Length: 574 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease homolog, mitochondrial
EC: 3.4.21.53
UniProt: P36776
Ligands: UFY, SO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	195	36% helix, 27% strand	P36776
B	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	187	36% helix, 27% strand	P36776
C	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	192	39% helix, 27% strand	P36776

Ligands and binding sites

UFY · N-[(1R)-1-borono-3-methylbutyl]-Nalpha-(pyrazine-2-carbonyl)-D-phenylalaninamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C

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

Pockets

5 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	999	0.77	0.79	74	empty
2	257	0.56	0.77	33	empty
3	100	0.47	0.80	32	UFY
4	103	0.45	0.79	29	UFY
5	73	0.36	0.77	17	empty

Interfaces

3 interfaces between chains.

A–B · 829 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 781 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 616 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6WZV · Lon protease proteolytic domain · the same entry in another collection · chain A against A, TM-score 1.00
P36776 · AlphaFold monomer V2.0 prediction for lon protease homolog, mitochondrial (P36776) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P36776
Elsewhere: RCSB PDB 6WZV · PDBe 6WZV · UniProt P36776

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.