MolNFT v1 · #121305 · protein + DNA
The crystal structure of ASFVPOLX(D51N MUTANT):DNA4 binary complex
5HRG · DNA polymerase beta-like protein: “The crystal structure of ASFVPOLX(D51N MUTANT):DNA4 binary complex”. X-ray diffraction, 2 ligands (MN, SO4), 1 pocket (best druggability 0.61). MolNFT v1 #121305 on GenesisL1: 3D structure, binding…
- PDB
- 5HRG
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 4
- 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*C)-3')
- UniProt
- A0A0A1E3N6
- Ligands
- MN, SO4
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase beta-like protein | protein | 177 | 34% helix, 33% strand | A0A0A1E3N6 |
| C, D | DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
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 | 216 | 0.61 | 0.82 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 567 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 560 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 373 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–D · 347 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 312 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5HRG · The crystal structure of AsfvPolX(D51N mutant):DNA4 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 5HRG · PDBe 5HRG · UniProt A0A0A1E3N6
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