Research workbench
3-methyladenine DNA-glycosylase from archaeoglobus fulgidus
Analyse 3-methyladenine DNA-glycosylase from archaeoglobus fulgidus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JHN
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyladenine DNA-glycosylase
- EC
- 3.2.2.21
- UniProt
- O28163
- Ligands
- MBO, NA, HG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-methyladenine DNA-glycosylase (EC 3.2.2.21) | protein | 293 | 52% helix, 14% strand | O28163 |
| B | 3-methyladenine DNA-glycosylase (EC 3.2.2.21) | protein | 291 | 53% helix, 14% strand | O28163 |
Ligands and binding sites
- MBO · Mercuribenzoic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- HG · Mercury (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.79 | 0.98 | 34 | GOL |
| 2 | 99 | 0.78 | 0.98 | 30 | GOL |
| 3 | 157 | 0.55 | 0.81 | 23 | empty |
| 4 | 162 | 0.52 | 0.79 | 21 | empty |
| 5 | 175 | 0.52 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2JHN · 3-methyladenine dna-glycosylase from Archaeoglobus fulgidus · 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 O28163
- Elsewhere: RCSB PDB 2JHN · PDBe 2JHN · UniProt O28163
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