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
- 5T3V
- 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
- MN, SO4
- Pockets
- 6 · 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 | 34% helix, 25% strand | Q9Y2C4 |
| B | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 300 | 35% helix, 24% strand | Q9Y2C4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.84 | 0.93 | 56 | empty |
| 2 | 405 | 0.59 | 0.75 | 35 | MN, SO4 |
| 3 | 253 | 0.53 | 0.76 | 24 | MN, SO4 |
| 4 | 64 | 0.30 | 0.74 | 17 | empty |
| 5 | 64 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2600 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- Q9Y2C4 · AlphaFold monomer V2.0 prediction for nuclease exog, mitochondrial (Q9Y2C4) · a predicted model of the same protein · chain B 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 5T3V · PDBe 5T3V · UniProt Q9Y2C4
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