Research workbench
Glp (G9A-like protein) set domain in complex with DNMT3AK44ME2 peptide
Analyse Glp (G9A-like protein) set domain in complex with DNMT3AK44ME2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SWC
- Type
- protein
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT1; DNA (cytosine-5)-methyltransferase 3A
- EC
- 2.1.1.-, 2.1.1.43, 2.1.1.37
- UniProt
- Q9H9B1, O88508
- Ligands
- SAH, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 261 | 10% helix, 26% strand | Q9H9B1 |
| P | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 9 | 0% helix, 11% strand | O88508 |
| Q | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 8 | 0% helix, 13% strand | O88508 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, P, B, Q
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.81 | 0.83 | 87 | empty |
| 2 | 194 | 0.53 | 0.78 | 24 | SAH |
| 3 | 186 | 0.53 | 0.78 | 24 | SAH |
| 4 | 72 | 0.45 | 0.82 | 19 | empty |
| 5 | 117 | 0.44 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1016 Ų buried · 15 hydrogen bonds · protein-protein
- B–Q · 714 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 660 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3SWC · GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9H9B1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT1 (Q9H9B1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O88508 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (O88508) · a predicted model of the same protein · chain P against A, TM-score 0.38
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 Q9H9B1
- Every structure of UniProt O88508
- Elsewhere: RCSB PDB 3SWC · PDBe 3SWC · UniProt Q9H9B1 · UniProt O88508
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