Research workbench
Structure of an unusual 3-methyladenine DNA glycosylase II (alka) from deinococcus radiodurans
Analyse Structure of an unusual 3-methyladenine DNA glycosylase II (alka) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YG8
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosidase II, putative
- UniProt
- Q9RRB0
- Ligands
- CL
- Pockets
- 8 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-3-methyladenine glycosidase II, putative | protein | 207 | 58% helix, 0% strand | Q9RRB0 |
| B | DNA-3-methyladenine glycosidase II, putative | protein | 206 | 60% helix, 0% strand | Q9RRB0 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.46 | 0.79 | 22 | empty |
| 2 | 114 | 0.44 | 0.78 | 17 | empty |
| 3 | 125 | 0.40 | 0.74 | 15 | empty |
| 4 | 124 | 0.39 | 0.74 | 16 | empty |
| 5 | 93 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 218 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2YG8 · Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus… · 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 Q9RRB0
- Elsewhere: RCSB PDB 2YG8 · PDBe 2YG8 · UniProt Q9RRB0
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