MolNFT v1 · #121310 · protein + DNA
The crystal structure of asfvpolx: 1NT-GAP(P) DNA2: dgtp ternary complex.
5HRL · DNA polymerase beta-like protein: “The crystal structure of asfvpolx: 1NT-GAP(P) DNA2: dgtp ternary complex.”. X-ray diffraction, 2 ligands (DGT, MN), 4 pockets (best druggability 0.65). MolNFT v1 #121310 on GenesisL1: 3D structure…
- PDB
- 5HRL
- Type
- protein + DNA
- Length
- 421 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
- 4 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 175 | 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 | 35% helix, 32% 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
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.65 | 0.75 | 56 | DGT, MN, GOL |
| 2 | 271 | 0.58 | 0.78 | 25 | empty |
| 3 | 123 | 0.50 | 0.81 | 19 | DGT, MN |
| 4 | 82 | 0.39 | 0.78 | 12 | empty |
Interfaces
13 interfaces between chains.
- A–C · 637 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 632 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–G · 419 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–D · 419 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- F–H · 357 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Compared structures
- 5HRL · The crystal structure of AsfvPolX: 1nt-gap(P) DNA2: dGTP ternary complex. · the same entry in another collection · chain C against C, 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 5HRL · PDBe 5HRL · UniProt A0A0A1E3N6
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