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
- 5T5C
- Type
- protein + DNA
- Length
- 624 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease exog, mitochondrial; DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3'); DNA…
- EC
- 3.1.30.-
- UniProt
- Q9Y2C4
- Ligands
- MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 296 | 33% helix, 25% strand | Q9Y2C4 |
| C, E | DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3') | dna | 8 | — | — |
| D, F | DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.83 | 0.92 | 62 | empty |
| 2 | 1012 | 0.76 | 0.78 | 64 | empty |
| 3 | 372 | 0.66 | 0.80 | 41 | empty |
| 4 | 340 | 0.63 | 0.79 | 29 | empty |
| 5 | 227 | 0.54 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2512 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 677 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 627 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–F · 459 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–D · 400 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5T5C · A Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y2C4 · AlphaFold monomer V2.0 prediction for nuclease exog, mitochondrial (Q9Y2C4) · 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 Q9Y2C4
- Elsewhere: RCSB PDB 5T5C · PDBe 5T5C · UniProt Q9Y2C4
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