MolNFT v1 · #107351 · protein
Crystal structure of DNMT3A-DNMT3L complex
4U7P · DNA (cytosine-5)-methyltransferase 3A: “Crystal structure of DNMT3A-DNMT3L complex”. X-ray diffraction, 2 ligands (SAH, ZN), 7 pockets (best druggability 0.62). MolNFT v1 #107351 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4U7P
- Type
- protein
- Length
- 623 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A; DNA (cytosine-5)-methyltransferase 3-like
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3
- Ligands
- SAH, ZN
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 426 | 30% helix, 16% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 197 | 32% helix, 18% strand | Q9UJW3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.62 | 0.76 | 53 | empty |
| 2 | 203 | 0.60 | 0.82 | 34 | SAH |
| 3 | 347 | 0.59 | 0.76 | 38 | empty |
| 4 | 203 | 0.52 | 0.77 | 29 | empty |
| 5 | 155 | 0.46 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 947 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4U7P · Crystal structure of DNMT3A-DNMT3L complex · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.97
- 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 0.71
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 4U7P · PDBe 4U7P · UniProt Q9Y6K1 · UniProt Q9UJW3
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