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P2C-state of wild type human mitochondrial LONP1 protease with bound endogenous substrate protein and in presence of ATP/ADP mix

Analyse P2C-state of wild type human mitochondrial LONP1 protease with bound endogenous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NGF
Type: protein
Length: 4,679 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease homolog, mitochondrial; Substrate protein CHAIN:G
EC: 3.4.21.53
UniProt: P36776
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 2 distinct chains · 44% helix, 9% 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 CHAIN:G	protein	23	0% helix, 0% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, B, C, D, E, F
ADP · Adenosine-5'-diphosphate · ligand · chains C
MG · Magnesium ion · metal · 5 copies · chains A, B, D, 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	662	0.88	0.92	98	ATP, MG
2	958	0.84	0.85	116	empty
3	400	0.82	0.90	69	empty
4	876	0.81	0.83	90	ATP, MG
5	452	0.81	0.89	72	empty

Interfaces

21 interfaces between chains.

A–B · 3022 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 2946 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2337 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 2295 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 2087 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7NGF · P2c-state of wild type human mitochondrial LONP1 protease with bound endogenous substrate… · 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 7NGF · PDBe 7NGF · UniProt P36776

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