Research workbench
Binary structure of escherichia COLI DNA adenine methyltransferase and S-adenosylhomocysteine
Analyse Binary structure of escherichia COLI DNA adenine methyltransferase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ORE
- Type
- protein
- Length
- 731 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA adenine methylase
- EC
- 2.1.1.72
- UniProt
- P0AEE8
- Ligands
- SAH, SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA adenine methylase (EC 2.1.1.72) | protein | 243 | 43% helix, 16% strand | P0AEE8 |
| E | DNA adenine methylase (EC 2.1.1.72) | protein | 244 | 41% helix, 15% strand | P0AEE8 |
| F | DNA adenine methylase (EC 2.1.1.72) | protein | 244 | 44% helix, 16% strand | P0AEE8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains D, E, F
- SO4 · Sulfate ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.62 | 0.78 | 51 | SAH |
| 2 | 296 | 0.59 | 0.78 | 35 | SAH |
| 3 | 261 | 0.58 | 0.78 | 33 | SAH |
| 4 | 55 | 0.31 | 0.77 | 15 | empty |
| 5 | 69 | 0.27 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–E · 441 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 429 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 425 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2ORE · Binary Structure of Escherichia coli DNA Adenine Methyltransferase and… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AEE8 · AlphaFold monomer V2.0 prediction for DNA adenine methylase (P0AEE8) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P0AEE8
- Elsewhere: RCSB PDB 2ORE · PDBe 2ORE · UniProt P0AEE8
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