Research workbench
Structure of DNMT3A (R882H) in complex with cgt DNA
Analyse Structure of DNMT3A (R882H) in complex with cgt DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8D
- Type
- protein + DNA
- Length
- 983 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A; DNA (cytosine-5)-methyltransferase 3-like; Cgt DNA…
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 284 | 32% helix, 18% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 187 | 35% helix, 16% strand | Q9UJW3 |
| D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 285 | 32% helix, 19% strand | Q9Y6K1 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 177 | 38% helix, 16% strand | Q9UJW3 |
| E, F | Cgt DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.74 | 0.89 | 29 | empty |
| 2 | 953 | 0.73 | 0.77 | 100 | SAH |
| 3 | 352 | 0.67 | 0.81 | 42 | SAH |
| 4 | 253 | 0.66 | 0.83 | 51 | empty |
| 5 | 214 | 0.57 | 0.80 | 23 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1147 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- A–D · 1008 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 875 Ų buried · 13 hydrogen bonds · protein-protein
- D–C · 874 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 863 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6W8D · Structure of DNMT3A (R882H) in complex with CGT DNA · the same entry in another collection · chain F against F, TM-score 1.00
- 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
- Q9UJW3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3-like (Q9UJW3) · a predicted model of the same protein · chain C against A, TM-score 0.96
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
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6W8D · PDBe 6W8D · UniProt Q9Y6K1 · UniProt Q9UJW3
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