Research workbench
Structure of human DNMT2, an enigmatic DNA methyltransferase homologue
Analyse Structure of human DNMT2, an enigmatic DNA methyltransferase homologue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G55
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA cytosine methyltransferase DNMT2
- EC
- 2.1.1.37
- UniProt
- O14717
- Ligands
- SAH, SO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cytosine methyltransferase DNMT2 (EC 2.1.1.37) | protein | 313 | 39% helix, 17% strand | O14717 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.56 | 0.79 | 38 | SAH |
| 2 | 70 | 0.29 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 2 modified, 1 covalent (oxidation, additive adduct).
Compared structures
- 1G55 · Structure of human DNMT2, an enigmatic DNA methyltransferase homologue · the same entry in another collection · chain A against A, TM-score 1.00
- O14717 · AlphaFold monomer V2.0 prediction for tRNA (CYTOSINE(38)-C(5))-methyltransferase (O14717) · a predicted model of the same protein · chain A 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 O14717
- Elsewhere: RCSB PDB 1G55 · PDBe 1G55 · UniProt O14717
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