Research workbench
Crystal structure of E. COLI DNA adenine methyltransferase in complex with aza-SAM
Analyse Crystal structure of E. COLI DNA adenine methyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GOM
- 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
- 0Y0
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 43% 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 | 42% helix, 17% strand | P0AEE8 |
| F | DNA adenine methylase (EC 2.1.1.72) | protein | 244 | 43% helix, 16% strand | P0AEE8 |
Ligands and binding sites
- 0Y0 · 5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine · ligand · 3 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.59 | 0.77 | 38 | 0Y0 |
| 2 | 304 | 0.59 | 0.78 | 40 | 0Y0 |
| 3 | 272 | 0.57 | 0.77 | 42 | 0Y0 |
| 4 | 83 | 0.36 | 0.76 | 17 | empty |
| 5 | 55 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–F · 444 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 437 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 430 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GOM · Crystal Structure of E. coli DNA Adenine Methyltransferase in Complex with Aza-SAM · 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 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 4GOM · PDBe 4GOM · UniProt P0AEE8
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