Research workbench
The crystal structure of ASFVPOLX(H115F/R127A mutant): 1NT-GAP(P) DNA2:DGTP ternary complex
Analyse The crystal structure of ASFVPOLX(H115F/R127A mutant): 1NT-GAP(P) DNA2:DGTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HRH
- Type
- protein + DNA
- Length
- 420 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*GP*TP*GP*TP*AP*CP*TP…
- UniProt
- A0A0A1E3N6
- Ligands
- DGT, MN
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 174 | 35% helix, 33% strand | A0A0A1E3N6 |
| C, F | DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*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 | — | — |
| B | DNA polymerase beta-like protein | protein | 176 | 34% helix, 34% strand | A0A0A1E3N6 |
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
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 | 877 | 0.79 | 0.82 | 90 | DGT, MN |
Interfaces
13 interfaces between chains.
- B–F · 612 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 608 Ų buried · 13 hydrogen bonds · protein-nucleic
- F–G · 410 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- C–D · 409 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- C–E · 357 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 5HRH · The crystal structure of AsfvPolX(H115F/R127A mutant): 1nt-gap(P) DNA2:dGTP ternary… · 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 5HRH · PDBe 5HRH · UniProt A0A0A1E3N6
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