MolNFT v1 · #183560 · protein
Crystal structure of mouse PRMT6 in complex with inhibitor EML736
7NUE · Protein arginine N-methyltransferase 6: “Crystal structure of mouse PRMT6 in complex with inhibitor EML736”. X-ray diffraction, 1 ligand (LSK), 3 pockets (best druggability 0.76). MolNFT v1 #183560 on GenesisL1: 3D structure…
- PDB
- 7NUE
- Type
- protein
- Length
- 652 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
- LSK
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 6 (EC 2.1.1.319) | protein | 335 | 31% helix, 37% strand | Q6NZB1 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.319) | protein | 317 | 29% helix, 37% strand | Q6NZB1 |
Ligands and binding sites
- LSK · methyl 6-[5-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]pentylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.76 | 0.83 | 57 | LSK |
| 2 | 239 | 0.67 | 0.84 | 36 | LSK |
| 3 | 73 | 0.50 | 0.84 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1797 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7NUE · Crystal structure of mouse PRMT6 in complex with inhibitor EML736 · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.98
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 7NUE · PDBe 7NUE · UniProt Q6NZB1
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