MolNFT v1 · #92542 · protein
Crystal structure of E. COLI DNA adenine methyltransferase in complex with sah
4GBE · DNA adenine methylase: “Crystal structure of E. COLI DNA adenine methyltransferase in complex with sah”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.64). MolNFT v1 #92542 on GenesisL1: 3D structure, binding…
- 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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