MolNFT v2 · #213235 · protein + DNA
The crystal structure of dG(Se-Sp)-DNA:Pol X product binary complex
8ILH · Repair DNA polymerase X: “The crystal structure of dG(Se-Sp)-DNA:Pol X product binary complex”. X-ray diffraction at 2.1, 4 ligands (GMS, 8EB, MG), 6 pockets (best druggability 0.75). MolNFT v2 #213235 on GenesisL1: 3D structure…
- PDB
- 8ILH
- Type
- protein + DNA
- Length
- 734 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- African swine fever virus (strain Badajoz 1971 Vero-adapted); SYNTHETIC…
- Molecule
- Repair DNA polymerase X; DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
- EC
- 2.7.7.7
- UniProt
- P42494
- Ligands
- GMS, 8EB, MG, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Repair DNA polymerase X (EC 2.7.7.7) | protein | 176 | 32% helix, 35% strand | P42494 |
| C, D | Repair DNA polymerase X (EC 2.7.7.7) | protein | 177 | 32% helix, 35% strand | P42494 |
| E, F, G, H | DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- GMS · 2'-deoxyguanosine-5'-monoselenophosphate · ligand · 3 copies · chains A, E, F, C, G, H, D
- 8EB · [[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] dihydrogen phosphate · ligand · chains B, E, F
- MG · Magnesium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
- SO4 · Sulfate ion · ion · 8 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.75 | 0.79 | 66 | MG, SO4, GMS |
| 2 | 50 | 0.65 | 0.96 | 16 | empty |
| 3 | 184 | 0.57 | 0.81 | 24 | empty |
| 4 | 164 | 0.55 | 0.81 | 22 | MG, SO4, GMS |
| 5 | 166 | 0.54 | 0.80 | 23 | 8EB, MG |
Interfaces
13 interfaces between chains.
- C–H · 589 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 581 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–E · 579 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–G · 541 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 295 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent (disulfide, covalent ligand).
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 P42494
- Elsewhere: RCSB PDB 8ILH · PDBe 8ILH · UniProt P42494
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