Research workbench
Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two cpg sites
Analyse Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BRR
- Type
- protein + DNA
- Length
- 981 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 · 29% 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 | 31% helix, 18% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 187 | 30% helix, 17% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 174 | 25% helix, 16% strand | Q9UJW3 |
| E, F | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.67 | 0.82 | 47 | SAH |
| 2 | 304 | 0.64 | 0.80 | 41 | SAH |
| 3 | 53 | 0.62 | 0.92 | 18 | empty |
| 4 | 190 | 0.62 | 0.83 | 20 | empty |
| 5 | 147 | 0.57 | 0.83 | 21 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1171 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–D · 975 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 931 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 930 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 778 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6BRR · Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites · 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 0.99
- 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 0.96
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 6BRR · PDBe 6BRR · UniProt Q9Y6K1 · UniProt Q9UJW3
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