Research workbench
Crystal structure of the mouse endonuclease ENDOG(H138A/SE-met)
Analyse Crystal structure of the mouse endonuclease ENDOG(H138A/SE-met) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYF
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- 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
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 218 | 22% helix, 33% strand | O08600 |
| C | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 218 | 25% helix, 31% strand | O08600 |
| D | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 222 | 25% helix, 31% strand | O08600 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.83 | 0.86 | 82 | MG |
| 2 | 211 | 0.75 | 0.90 | 33 | empty |
| 3 | 177 | 0.75 | 0.91 | 32 | empty |
| 4 | 53 | 0.61 | 0.93 | 18 | empty |
| 5 | 91 | 0.57 | 0.86 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2526 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2458 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 780 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 6LYF · Crystal structure of the mouse endonuclease EndoG(H138A/Se-Met) · 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 D 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 6LYF · PDBe 6LYF · UniProt O08600
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