MolNFT v1 · #121303 · protein + DNA
The crystal structure of ASFVPOLX:DNA3 binary complex
5HRE · DNA polymerase beta-like protein: “The crystal structure of ASFVPOLX:DNA3 binary complex”. X-ray diffraction, 2 ligands (MN, PO4), 1 pocket (best druggability 0.53). MolNFT v1 #121303 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HRE
- Type
- protein + DNA
- Length
- 185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta-like protein; DNA (5'-D(P*AP*GP*GP*AP*TP*CP*CP*T)-3')
- UniProt
- A0A0A1E3N6
- Ligands
- MN, PO4
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 177 | 33% helix, 34% strand | A0A0A1E3N6 |
| B | DNA (5'-D(P*AP*GP*GP*AP*TP*CP*CP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.53 | 0.78 | 29 | FMT |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5HRE · The crystal structure of AsfvPolX:DNA3 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 5HRE · PDBe 5HRE · UniProt A0A0A1E3N6
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