MolNFT v1 · #156415 · protein
Crystal structure of the mouse endonuclease ENDOG(H138A/C110A), space group P212121
6M3F · Endonuclease G, mitochondrial: “Crystal structure of the mouse endonuclease ENDOG(H138A/C110A), space group P212121”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.74). MolNFT v1 #156415 on GenesisL1: 3D…
- PDB
- 6M3F
- Type
- protein
- Length
- 438 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
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 223 | 28% helix, 30% strand | O08600 |
| C | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 215 | 25% helix, 31% strand | O08600 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.74 | 0.89 | 42 | empty |
| 2 | 50 | 0.43 | 0.84 | 17 | empty |
| 3 | 54 | 0.43 | 0.83 | 17 | empty |
| 4 | 89 | 0.36 | 0.75 | 17 | MG |
| 5 | 93 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- B–C · 2660 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6M3F · Crystal structure of the mouse endonuclease EndoG(H138A/C110A), space group P212121 · the same entry in another collection · chain B against B, 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 0.99
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 6M3F · PDBe 6M3F · UniProt O08600
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