Research workbench
The crystal structure of ASFVPOLX:DNA1 binary complex
Analyse The crystal structure of ASFVPOLX:DNA1 binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HRB
- Type
- protein + DNA
- Length
- 193 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta-like protein; DNA (5'-D(*CP*GP*GP*AP*TP*AP*TP*CP*C)-3')
- UniProt
- A0A0A1E3N6
- Ligands
- MN
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 176 | 35% helix, 35% strand | A0A0A1E3N6 |
| D | DNA (5'-D(*CP*GP*GP*AP*TP*AP*TP*CP*C)-3') | dna | 9 | — | — |
| E | DNA (5'-D(*CP*GP*GP*AP*TP*AP*TP*CP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, D
- GOL · Glycerol · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.37 | 0.79 | 12 | BME |
| 2 | 52 | 0.34 | 0.79 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–E · 665 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 344 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–E · 341 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 5HRB · The crystal structure of AsfvPolX:DNA1 binary complex · 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 A0A0A1E3N6
- Elsewhere: RCSB PDB 5HRB · PDBe 5HRB · UniProt A0A0A1E3N6
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