Research workbench
The crystal structure of dG-DNA:Pol X product binary complex
Analyse The crystal structure of dG-DNA:Pol X product binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ILG
- Type
- protein + DNA
- Length
- 384 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.805
- 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*CP*G)-3')
- EC
- 2.7.7.7
- UniProt
- P42494
- Ligands
- MN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.805 · 2 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Repair DNA polymerase X (EC 2.7.7.7) | protein | 176 | 33% helix, 34% strand | P42494 |
| D, E, C, F | DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, D, B, C
- FMT · Formic acid · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.73 | 0.76 | 72 | MN, FMT |
| 2 | 109 | 0.43 | 0.78 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–E · 601 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 590 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–F · 387 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- D–E · 387 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- B–C · 358 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 8ILG · PDBe 8ILG · UniProt P42494
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