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
- 5HRI
- Type
- protein + DNA
- Length
- 421 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta-like protein; DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*CP*TP*GP*TP*AP*CP*TP…
- UniProt
- A0A0A1E3N6
- Ligands
- DGT, MN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 175 | 33% helix, 33% strand | A0A0A1E3N6 |
| B | DNA polymerase beta-like protein | protein | 176 | 32% helix, 33% strand | A0A0A1E3N6 |
| C, F | DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*CP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3' | dna | 18 | — | — |
| D, G | DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3') | dna | 9 | — | — |
| E, H | DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, C, D, B, F, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.66 | 0.76 | 53 | DGT, MN |
| 2 | 269 | 0.57 | 0.78 | 27 | empty |
| 3 | 173 | 0.52 | 0.79 | 26 | DGT, MN |
| 4 | 58 | 0.35 | 0.78 | 11 | empty |
Interfaces
12 interfaces between chains.
- A–C · 648 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 639 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 413 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- F–G · 407 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- C–E · 354 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 5HRI · 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 5HRI · PDBe 5HRI · UniProt A0A0A1E3N6
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