Research workbench
Crystal structure of mouse PRMT6 in complex with inhibitor U1
Analyse Crystal structure of mouse PRMT6 in complex with inhibitor U1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SQ3
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 6
- EC
- 2.1.1.319
- UniProt
- Q6NZB1
- Ligands
- 6RE
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 6 (EC 2.1.1.319) | protein | 322 | 30% helix, 37% strand | Q6NZB1 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.319) | protein | 319 | 28% helix, 36% strand | Q6NZB1 |
Ligands and binding sites
- 6RE · [[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3, 4-bis(oxidanyl)oxolan-2-yl]ethylamino]-azanyl-methylidene]azanium · ligand · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.73 | 0.87 | 41 | 6RE |
| 2 | 258 | 0.67 | 0.83 | 36 | 6RE |
| 3 | 110 | 0.54 | 0.83 | 16 | empty |
| 4 | 104 | 0.50 | 0.81 | 18 | empty |
| 5 | 51 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1780 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6SQ3 · Crystal structure of mouse PRMT6 in complex with inhibitor U1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NZB1 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q6NZB1) · a predicted model of the same protein · chain A 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 Q6NZB1
- Elsewhere: RCSB PDB 6SQ3 · PDBe 6SQ3 · UniProt Q6NZB1
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