MolNFT v1 · #134451 · protein + DNA
A novel domain in human exog converts apoptotic endonuclease to DNA- repair enzyme
5T4I · Nuclease exog, mitochondrial: “A novel domain in human exog converts apoptotic endonuclease to DNA- repair enzyme”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.84). MolNFT v1 #134451 on GenesisL1: 3D structure…
- PDB
- 5T4I
- Type
- protein + DNA
- Length
- 631 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
- MN
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 297 | 33% helix, 25% strand | Q9Y2C4 |
| B | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 298 | 36% helix, 24% strand | Q9Y2C4 |
| C, E | DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3') | dna | 9 | — | — |
| D, F | DNA (5'-D(*GP*CP*AP*CP*GP*TP*CP*AP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, E, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.84 | 0.92 | 59 | empty |
| 2 | 907 | 0.76 | 0.79 | 71 | empty |
| 3 | 897 | 0.75 | 0.79 | 69 | empty |
| 4 | 186 | 0.47 | 0.75 | 22 | empty |
| 5 | 133 | 0.41 | 0.75 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2558 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 651 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 643 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 465 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- E–F · 462 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5T4I · 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 5T4I · PDBe 5T4I · UniProt Q9Y2C4
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