MolNFT v1 · #183149 · protein

P2A-state of wild type human mitochondrial LONP1 protease with bound substrate protein and in presence of atpgs

7NGC · Lon protease homolog, mitochondrial: “P2A-state of wild type human mitochondrial LONP1 protease with bound substrate protein and in presence of…”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.87).…

PDB: 7NGC
Type: protein
Length: 4,685 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease homolog, mitochondrial; Substrate protein
EC: 3.4.21.53
UniProt: P36776
Ligands: AGS, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 43% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	776	45% helix, 9% strand	P36776
G	Substrate protein	protein	29	0% helix, 0% strand	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E, F
ADP · Adenosine-5'-diphosphate · ligand · chains D
MG · Magnesium ion · metal · 5 copies · chains A, B, C, E, F

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	708	0.87	0.91	107	MG
2	938	0.83	0.85	95	empty
3	520	0.82	0.88	78	empty
4	136	0.81	0.97	39	empty
5	538	0.81	0.87	73	empty

Interfaces

21 interfaces between chains.

A–B · 2897 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2791 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 2490 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2177 Å² buried · 20 hydrogen bonds · protein-protein
A–F · 2043 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7NGC · P2a-state of wild type human mitochondrial LONP1 protease with bound substrate protein… · 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 P36776
Elsewhere: RCSB PDB 7NGC · PDBe 7NGC · UniProt P36776

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