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Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer
Analyse Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8TE1
- Type
- protein
- Length
- 1,748 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.48
- Source
- Homo sapiens
- Molecule
- DNA (cytosine-5)-methyltransferase 3A
- EC
- 2.1.1.37, 2.1.1.-
- UniProt
- Q9Y6K1
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.48 · 6 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 273 | 32% helix, 18% strand | Q9Y6K1 |
| B, C, D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 275 | 32% helix, 19% strand | Q9Y6K1 |
| E | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 159 | 35% helix, 27% strand | Q9Y6K1 |
| H | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 161 | 35% helix, 27% strand | Q9Y6K1 |
| F | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 160 | 34% helix, 25% strand | Q9Y6K1 |
| G | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37, 2.1.1.-) | protein | 170 | 34% helix, 24% strand | Q9Y6K1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.84 | 0.85 | 99 | empty |
| 2 | 348 | 0.66 | 0.80 | 58 | SAH |
| 3 | 496 | 0.65 | 0.77 | 37 | empty |
| 4 | 481 | 0.63 | 0.76 | 45 | empty |
| 5 | 227 | 0.62 | 0.82 | 41 | SAH |
Interfaces
11 interfaces between chains.
- C–D · 963 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 946 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 926 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 908 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 882 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- Q9Y6K1 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) · 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 Q9Y6K1
- Elsewhere: RCSB PDB 8TE1 · PDBe 8TE1 · UniProt Q9Y6K1
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