Research workbench
Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site.
Analyse Structure of aminofluorene adduct paired opposite cytosine at the polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UA1
- Type
- protein + DNA
- Length
- 603 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
- UniProt
- P52026
- Ligands
- AF, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 11 | — | — |
| C | DNA template strand with aminofluorene adduct | dna | 12 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | P52026 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.72 | 0.76 | 76 | AF, SO4 |
| 2 | 432 | 0.71 | 0.82 | 48 | empty |
| 3 | 268 | 0.71 | 0.86 | 32 | empty |
| 4 | 223 | 0.64 | 0.82 | 24 | empty |
| 5 | 53 | 0.52 | 0.88 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–A · 887 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–A · 834 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 486 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1UA1 · Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. · the same entry in another collection · chain B against B, TM-score 1.00
- P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P52026
- Elsewhere: RCSB PDB 1UA1 · PDBe 1UA1 · UniProt P52026
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