Research workbench
C-terminal His tagged apPOL exonuclease mutant
Analyse C-terminal His tagged apPOL exonuclease mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DKU
- Type
- protein
- Length
- 1,158 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Plasmodium falciparum (isolate 3D7)
- Molecule
- Prex DNA polymerase
- EC
- 2.7.7.7
- UniProt
- Q8ILY1
- Ligands
- MG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prex DNA polymerase (EC 2.7.7.7) | protein | 577 | 50% helix, 17% strand | Q8ILY1 |
| B | Prex DNA polymerase (EC 2.7.7.7) | protein | 581 | 50% helix, 17% strand | Q8ILY1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.84 | 0.84 | 89 | empty |
| 2 | 766 | 0.81 | 0.84 | 79 | empty |
| 3 | 583 | 0.70 | 0.78 | 57 | MG |
| 4 | 501 | 0.69 | 0.79 | 58 | MG |
| 5 | 59 | 0.52 | 0.87 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DKU · C-terminal his tagged appol exonuclease mutant · the same entry in another collection · 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 Q8ILY1
- Elsewhere: RCSB PDB 5DKU · PDBe 5DKU · UniProt Q8ILY1
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