MolNFT v1 · #121309 · protein + DNA
The crystal structure of ASFVPOLX(H115F mutant): 1NT-GAP(P) DNA2:DGTP ternary complex
5HRK · DNA polymerase beta-like protein: “The crystal structure of ASFVPOLX(H115F mutant): 1NT-GAP(P) DNA2:DGTP ternary complex”. X-ray diffraction, 3 ligands (DGT, MN, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #121309 on…
- PDB
- 5HRK
- 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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3'); DNA (5'…
- UniProt
- A0A0A1E3N6
- Ligands
- DGT, MN, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 174 | 32% helix, 32% strand | A0A0A1E3N6 |
| B | DNA polymerase beta-like protein | protein | 176 | 33% helix, 30% strand | A0A0A1E3N6 |
| F, C | DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3') | dna | 9 | — | — |
| H, E | DNA (5'- D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3') | dna | 18 | — | — |
| G, D | DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, F, H, B, C, E
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.75 | 0.78 | 79 | DGT, MN |
| 2 | 464 | 0.73 | 0.83 | 53 | DGT, MN |
| 3 | 100 | 0.63 | 0.88 | 26 | empty |
| 4 | 74 | 0.54 | 0.86 | 21 | empty |
Interfaces
13 interfaces between chains.
- A–H · 581 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–E · 559 Ų buried · 13 hydrogen bonds · protein-nucleic
- F–H · 425 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- C–E · 411 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- E–D · 351 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5HRK · The crystal structure of AsfvPolX(H115F mutant): 1nt-gap(P) DNA2:dGTP ternary complex · the same entry in another collection · chain H against H, 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 5HRK · PDBe 5HRK · UniProt A0A0A1E3N6
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