MolNFT v1 · #168200 · protein + DNA
Structure of DNMT3A (R882H) in complex with cag DNA
6W8J · DNA (cytosine-5)-methyltransferase 3A: “Structure of DNMT3A (R882H) in complex with cag DNA”. X-ray diffraction, 1 ligand (SAH), 17 pockets (best druggability 0.77). MolNFT v1 #168200 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6W8J
- Type
- protein + DNA
- Length
- 988 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; Cag DNA…
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3
- Ligands
- SAH
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 33% 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 | 193 | 33% helix, 15% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 178 | 33% helix, 15% strand | Q9UJW3 |
| D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 285 | 33% helix, 18% strand | Q9Y6K1 |
| E, F | Cag DNA (25-mer) | dna | 24 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.77 | 0.80 | 101 | empty |
| 2 | 430 | 0.76 | 0.85 | 53 | empty |
| 3 | 220 | 0.66 | 0.84 | 38 | SAH |
| 4 | 243 | 0.64 | 0.82 | 39 | SAH |
| 5 | 164 | 0.59 | 0.82 | 27 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1096 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- A–D · 995 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 909 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 834 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6W8J · Structure of DNMT3A (R882H) in complex with CAG DNA · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.95
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 6W8J · PDBe 6W8J · UniProt Q9Y6K1 · UniProt Q9UJW3
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