Research workbench
Crystal structure of DNMT3A add domain G550D mutant bound to H3 peptide
Analyse Crystal structure of DNMT3A add domain G550D mutant 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
- 4QBR
- Type
- protein
- Length
- 286 residues
- Chains
- 4
- 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
- 1 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 136 | 34% helix, 15% strand | Q9Y6K1 |
| P, E | Histone H3 | protein | 7 | 0% helix, 57% 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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.46 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 705 Ų buried · 4 hydrogen bonds · protein-protein
- A–P · 593 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 566 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4QBR · Crystal structure of DNMT3a ADD domain G550D mutant 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 A against A, TM-score 0.98
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 4QBR · PDBe 4QBR · UniProt Q9Y6K1
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