MolNFT v1 · #111393 · protein

Crystal structure of a hexameric lona protease bound to three adps

4YPL · Lon protease: “Crystal structure of a hexameric lona protease bound to three adps”. X-ray diffraction, 2 ligands (4KZ, ADP), 20 pockets (best druggability 0.83). MolNFT v1 #111393 on GenesisL1: 3D structure, binding sites and…

PDB: 4YPL
Type: protein
Length: 3,224 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease
EC: 3.4.21.53
UniProt: A0A059VAZ3
Ligands: 4KZ, ADP
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Lon protease (EC 3.4.21.53)	protein	537	42% helix, 16% strand	A0A059VAZ3
C	Lon protease (EC 3.4.21.53)	protein	538	39% helix, 16% strand	A0A059VAZ3
F	Lon protease (EC 3.4.21.53)	protein	538	44% helix, 16% strand	A0A059VAZ3

Ligands and binding sites

4KZ · N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 6 copies · chains A, B, C, F, D, E
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, F, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1197	0.83	0.84	129	ADP
2	1022	0.83	0.84	109	empty
3	913	0.82	0.84	102	empty
4	992	0.81	0.82	107	empty
5	969	0.81	0.82	89	empty

Interfaces

9 interfaces between chains.

B–C · 2392 Å² buried · 21 hydrogen bonds · protein-protein
A–F · 2241 Å² buried · 26 hydrogen bonds · protein-protein
D–E · 2130 Å² buried · 20 hydrogen bonds · protein-protein
F–E · 1885 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1681 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

4YPL · Crystal structure of a hexameric LonA protease bound to three ADPs · 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 A0A059VAZ3
Elsewhere: RCSB PDB 4YPL · PDBe 4YPL · UniProt A0A059VAZ3

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