Research workbench
Crystal structure of E. COLI DNA adenine methyltransferase in complex with sah
Analyse Crystal structure of E. COLI DNA adenine methyltransferase in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GBE
- 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
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA adenine methylase (EC 2.1.1.72) | protein | 243 | 44% helix, 17% strand | P0AEE8 |
| E | DNA adenine methylase (EC 2.1.1.72) | protein | 244 | 43% helix, 17% strand | P0AEE8 |
| F | DNA adenine methylase (EC 2.1.1.72) | protein | 244 | 43% helix, 16% strand | P0AEE8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.64 | 0.78 | 45 | SAH |
| 2 | 297 | 0.61 | 0.79 | 35 | SAH |
| 3 | 296 | 0.61 | 0.78 | 32 | SAH |
| 4 | 71 | 0.35 | 0.77 | 15 | empty |
| 5 | 74 | 0.35 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- D–F · 441 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 429 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 423 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GBE · Crystal Structure of E. coli DNA Adenine Methyltransferase in Complex with SAH · the same entry in another collection · chain E against E, TM-score 1.00
- P0AEE8 · AlphaFold monomer V2.0 prediction for DNA adenine methylase (P0AEE8) · a predicted model of the same protein · chain E 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 4GBE · PDBe 4GBE · UniProt P0AEE8
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