MolNFT v1 · #18600 · protein
Crystal structure of H.PYLORI 3-methyladenine DNA glycosylase (magiii) bound to 1,N6-ethenoadenine
1PU8: “Crystal structure of H.PYLORI 3-methyladenine DNA glycosylase (magiii) bound to 1,N6-ethenoadenine”. X-ray diffraction, 1 ligand (EA1), 3 pockets (best druggability 0.52). MolNFT v1 #18600 on GenesisL1: 3D structure, binding sites…
- PDB
- 1PU8
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyladenine DNA glycosylase
- UniProt
- O25323
- Ligands
- EA1
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-methyladenine DNA glycosylase | protein | 215 | 65% helix, 0% strand | O25323 |
Ligands and binding sites
- EA1 · 3H-imidazo[2,1-i]purine · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.52 | 0.80 | 25 | EA1 |
| 2 | 136 | 0.52 | 0.80 | 24 | EA1 |
| 3 | 50 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, carboxylation).
Compared structures
- 1PU8 · Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to… · the same entry in another collection · chain A against A, 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 O25323
- Elsewhere: RCSB PDB 1PU8 · PDBe 1PU8 · UniProt O25323
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