Research workbench
3-methyladenine DNA glycosylase II from escherichia COLI
Analyse 3-methyladenine DNA glycosylase II from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MPG
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyladenine DNA glycosylase II
- EC
- 3.2.2.21
- UniProt
- P04395
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-methyladenine DNA glycosylase II (EC 3.2.2.21) | protein | 282 | 49% helix, 11% strand | P04395 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.63 | 0.78 | 37 | empty |
| 2 | 205 | 0.61 | 0.82 | 27 | empty |
| 3 | 209 | 0.61 | 0.82 | 30 | empty |
| 4 | 124 | 0.52 | 0.81 | 21 | empty |
| 5 | 125 | 0.52 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 382 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1MPG · 3-methyladenine DNA glycosylase II from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
- P04395 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase 2 (P04395) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P04395
- Elsewhere: RCSB PDB 1MPG · PDBe 1MPG · UniProt P04395
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