MolNFT v1 · #148390 · protein + DNA
Crystal structure of DNMT3A-DNMT3L in complex with single cpg- containing DNA
6F57 · DNA (cytosine-5)-methyltransferase 3A: “Crystal structure of DNMT3A-DNMT3L in complex with single cpg- containing DNA”. X-ray diffraction, 1 ligand (SAH), 14 pockets (best druggability 0.76). MolNFT v1 #148390 on GenesisL1: 3D…
- PDB
- 6F57
- Type
- protein + DNA
- Length
- 909 residues
- Chains
- 8
- 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
- 14 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 285 | 31% helix, 19% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 150 | 32% helix, 18% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 151 | 33% helix, 16% strand | Q9UJW3 |
| D | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 283 | 31% helix, 18% strand | Q9Y6K1 |
| E, G | DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') | dna | 10 | — | — |
| F, H | DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.76 | 0.85 | 56 | empty |
| 2 | 270 | 0.69 | 0.84 | 45 | SAH |
| 3 | 321 | 0.67 | 0.82 | 51 | SAH |
| 4 | 155 | 0.60 | 0.84 | 20 | empty |
| 5 | 142 | 0.57 | 0.83 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–D · 965 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 899 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 837 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–H · 823 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6F57 · Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA · the same entry in another collection · chain H against H, 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 D 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 6F57 · PDBe 6F57 · UniProt Q9Y6K1 · UniProt Q9UJW3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.