Research workbench
The crystal structure of asfvpolx: DNA5: dgtp ternary complex
Analyse The crystal structure of asfvpolx: DNA5: dgtp ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HRF
- 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(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3')
- UniProt
- A0A0A1E3N6
- Ligands
- DGT, MN, SO4
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 178 | 33% helix, 33% strand | A0A0A1E3N6 |
| B | DNA polymerase beta-like protein | protein | 174 | 33% helix, 32% strand | A0A0A1E3N6 |
| C, D | DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3') | dna | 9 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, C, D, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.55 | 0.80 | 23 | MN, DGT |
| 2 | 164 | 0.55 | 0.81 | 24 | MN, DGT |
| 3 | 61 | 0.31 | 0.76 | 14 | empty |
| 4 | 57 | 0.28 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 575 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 558 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 357 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- A–D · 169 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 144 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5HRF · The crystal structure of AsfvPolX: DNA5: dGTP ternary 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 5HRF · PDBe 5HRF · UniProt A0A0A1E3N6
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