MolNFT v1 · #121302 · protein + DNA
The crystal structure of ASFVPOLX:DNA2 binary complex
5HRD · DNA polymerase beta-like protein: “The crystal structure of ASFVPOLX:DNA2 binary complex”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.71). MolNFT v1 #121302 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HRD
- Type
- protein + DNA
- Length
- 738 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta-like protein; DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
- UniProt
- A0A0A1E3N6
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase beta-like protein | protein | 176 | 33% helix, 34% strand | A0A0A1E3N6 |
| C, D | DNA polymerase beta-like protein | protein | 177 | 33% helix, 33% strand | A0A0A1E3N6 |
| E, F, G, H | DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.71 | 0.75 | 51 | empty |
| 2 | 248 | 0.69 | 0.85 | 33 | empty |
| 3 | 65 | 0.34 | 0.77 | 14 | empty |
Interfaces
13 interfaces between chains.
- C–H · 581 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 579 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 554 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–G · 495 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 376 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5HRD · The crystal structure of AsfvPolX:DNA2 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 5HRD · PDBe 5HRD · UniProt A0A0A1E3N6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.