Research workbench
Crystal structure of DNMT3A add domain bound to H3 peptide
Analyse Crystal structure of DNMT3A add domain bound to H3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QBQ
- Type
- protein
- Length
- 282 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A; Histone H3
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 137 | 32% helix, 15% strand | Q9Y6K1 |
| P | Histone H3 | protein | 8 | 0% helix, 38% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.72 | 0.97 | 18 | empty |
| 2 | 386 | 0.63 | 0.78 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–C · 672 Ų buried · 10 hydrogen bonds · protein-protein
- C–P · 558 Ų buried · 12 hydrogen bonds · protein-protein
- A–P · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4QBQ · Crystal structure of DNMT3a ADD domain bound to H3 peptide · 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 C against A, TM-score 0.97
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 4QBQ · PDBe 4QBQ · UniProt Q9Y6K1
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