Research workbench
Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase
Analyse Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UA0
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer strand; DNA template strand with aminofluorene adduct; DNA polymerase I
- EC
- 2.7.7.7
- Ligands
- AF, GLC, FRU, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 9 | — | — |
| C | DNA template strand with aminofluorene adduct | dna | 12 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 54% helix, 13% strand | — |
Ligands and binding sites
- AF · 2-aminofluorene · ligand · chains C, A
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.72 | 0.87 | 30 | empty |
| 2 | 368 | 0.70 | 0.82 | 47 | GLC, FRU |
| 3 | 614 | 0.65 | 0.76 | 54 | empty |
| 4 | 218 | 0.62 | 0.82 | 34 | AF |
| 5 | 137 | 0.46 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1135 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–A · 841 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 431 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1UA0 · Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 1UA0 · PDBe 1UA0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.