Research workbench
A novel domain in human exog converts apoptotic endonuclease to DNA- repair enzyme
Analyse A novel domain in human exog converts apoptotic endonuclease to DNA- repair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T40
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease exog, mitochondrial
- EC
- 3.1.30.-
- UniProt
- Q9Y2C4
- Ligands
- MG, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 299 | 33% helix, 24% strand | Q9Y2C4 |
| B | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 300 | 35% helix, 24% strand | Q9Y2C4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.84 | 0.93 | 59 | empty |
| 2 | 470 | 0.61 | 0.75 | 40 | SO4, MG |
| 3 | 362 | 0.57 | 0.75 | 38 | SO4, MG |
| 4 | 58 | 0.30 | 0.75 | 13 | empty |
| 5 | 50 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2583 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5T40 · A Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2C4 · AlphaFold monomer V2.0 prediction for nuclease exog, mitochondrial (Q9Y2C4) · a predicted model of the same protein · 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 Q9Y2C4
- Elsewhere: RCSB PDB 5T40 · PDBe 5T40 · UniProt Q9Y2C4
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