MolNFT v1 · #38661 · protein
Crystal structure of DNA-3-methyladenine glycosidase (10174367) from bacillus halodurans at 2.55 a resolution
2H56: “Crystal structure of DNA-3-methyladenine glycosidase (10174367) from bacillus halodurans at 2.55 a resolution”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #38661 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2H56
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosidase
- EC
- 3.2.2.-
- UniProt
- Q9KC25
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-3-methyladenine glycosidase (EC 3.2.2.-) | protein | 218 | 62% helix, 4% strand | Q9KC25 |
| B | DNA-3-methyladenine glycosidase (EC 3.2.2.-) | protein | 217 | 62% helix, 3% strand | Q9KC25 |
| C | DNA-3-methyladenine glycosidase (EC 3.2.2.-) | protein | 204 | 61% helix, 3% strand | Q9KC25 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.63 | 0.84 | 26 | empty |
| 2 | 220 | 0.55 | 0.78 | 27 | empty |
| 3 | 125 | 0.46 | 0.78 | 18 | empty |
| 4 | 159 | 0.45 | 0.76 | 26 | empty |
| 5 | 191 | 0.45 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 372 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 287 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2H56 · Crystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans… · 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 Q9KC25
- Elsewhere: RCSB PDB 2H56 · PDBe 2H56 · UniProt Q9KC25
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