Research workbench
Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site
Analyse Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KDA
- Type
- protein + DNA
- Length
- 989 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.909
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA (cytosine-5)-methyltransferase 3B; DNA (cytosine-5)-methyltransferase 3-like; DNA…
- EC
- 2.1.1.37
- UniProt
- Q9UBC3, Q9UJW3
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.909 · 4 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) | protein | 284 | 32% helix, 18% strand | Q9UBC3 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 188 | 35% helix, 18% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 183 | 34% 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, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.70 | 0.84 | 50 | SAH |
| 2 | 216 | 0.66 | 0.85 | 37 | SAH |
| 3 | 464 | 0.66 | 0.78 | 48 | empty |
| 4 | 418 | 0.62 | 0.77 | 40 | empty |
| 5 | 286 | 0.55 | 0.76 | 40 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1057 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–D · 955 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 934 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 827 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6KDA · Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing cpgpg site · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UBC3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) · 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 0.97
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 Q9UBC3
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6KDA · PDBe 6KDA · UniProt Q9UBC3 · UniProt Q9UJW3
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