MolNFT v1 · #158094 · protein

Mouse endonuclease G mutant - H97A

6NJT · Endonuclease G, mitochondrial: “Mouse endonuclease G mutant - H97A”. X-ray diffraction, 2 ligands (MG, CL), 6 pockets (best druggability 0.74). MolNFT v1 #158094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NJT
Type: protein
Length: 451 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease G, mitochondrial
EC: 3.1.30.-
UniProt: O08600
Ligands: MG, CL
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endonuclease G, mitochondrial (EC 3.1.30.-)	protein	225	29% helix, 30% strand	O08600
B	Endonuclease G, mitochondrial (EC 3.1.30.-)	protein	226	25% helix, 31% strand	O08600

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 11 copies · chains A, B
IPA · Isopropyl alcohol · additive · 8 copies · chains A, B

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

Pockets

6 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	318	0.74	0.86	54	empty
2	79	0.67	0.92	25	empty
3	145	0.48	0.78	23	MG, CL
4	159	0.47	0.77	22	MG, CL
5	53	0.46	0.85	17	empty

Interfaces

1 interface between chains.

A–B · 2773 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6NJT · Mouse endonuclease G mutant - H97A · the same entry in another collection · chain A against A, TM-score 1.00
O08600 · AlphaFold monomer V2.0 prediction for endonuclease G, mitochondrial (O08600) · 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 O08600
Elsewhere: RCSB PDB 6NJT · PDBe 6NJT · UniProt O08600

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