MolNFT v1 · #141129 · protein + DNA
Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two cpg sites
5YX2 · DNA (cytosine-5)-methyltransferase 3A: “Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two cpg sites”. X-ray diffraction, 1 ligand (SAH), 16 pockets (best druggability 0.67). MolNFT v1 #141129 on GenesisL1: 3D…
- PDB
- 5YX2
- Type
- protein + DNA
- Length
- 982 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; DNA…
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 285 | 33% helix, 18% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 188 | 34% helix, 16% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 174 | 30% helix, 18% strand | Q9UJW3 |
| E, F | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
- GOL · Glycerol · additive · 6 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.67 | 0.82 | 44 | GOL, SAH |
| 2 | 327 | 0.66 | 0.81 | 44 | SAH, GOL |
| 3 | 60 | 0.62 | 0.91 | 18 | empty |
| 4 | 129 | 0.53 | 0.82 | 20 | empty |
| 5 | 150 | 0.50 | 0.79 | 19 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1163 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–D · 974 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 929 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 920 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 809 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5YX2 · Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites · 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 5YX2 · PDBe 5YX2 · UniProt Q9Y6K1 · UniProt Q9UJW3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.