Research workbench
Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and an aryl pyrazole inhibitor
Analyse Crystal structure of human protein arginine methyltransferase PRMT6 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y2H
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.37
- Source
- Homo sapiens
- Molecule
- Protein arginine N-methyltransferase 6
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q96LA8
- Ligands
- SAH, 49K
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.37 · 2 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 337 | 31% helix, 35% strand | Q96LA8 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 352 | 34% helix, 34% strand | Q96LA8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 49K · N-{[5-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-N-methylethane-1,2-diamine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.76 | 0.83 | 67 | SAH, 49K, GOL |
| 2 | 343 | 0.72 | 0.84 | 48 | SAH, 49K |
| 3 | 114 | 0.45 | 0.78 | 25 | empty |
| 4 | 68 | 0.31 | 0.74 | 14 | empty |
| 5 | 50 | 0.29 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1833 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4Y2H · Crystal structure of human protein arginine methyltransferase PRMT6 bound to sah and an… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96LA8 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q96LA8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q96LA8
- Elsewhere: RCSB PDB 4Y2H · PDBe 4Y2H · UniProt Q96LA8
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