Research workbench
8OXOGUANINE at the pre-insertion site of the polymerase active site
Analyse 8OXOGUANINE at the pre-insertion site of the polymerase active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U45
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer strand; DNA template strand with 8-oxoguanine; DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- P52026
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 9 | — | — |
| C | DNA template strand with 8-oxoguanine | dna | 11 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | P52026 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.69 | 0.81 | 43 | GLC, FRU |
| 2 | 194 | 0.67 | 0.86 | 31 | empty |
| 3 | 701 | 0.67 | 0.76 | 66 | SO4, MG |
| 4 | 110 | 0.43 | 0.77 | 26 | empty |
| 5 | 108 | 0.38 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1238 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–A · 807 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 436 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 1U45 · PDBe 1U45 · UniProt P52026
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