MolNFT v1 · #183559 · protein
Crystal structure of mouse PRMT6 in complex with inhibitor EML734
7NUD · Protein arginine N-methyltransferase 6: “Crystal structure of mouse PRMT6 in complex with inhibitor EML734”. X-ray diffraction, 1 ligand (LRZ), 4 pockets (best druggability 0.75). MolNFT v1 #183559 on GenesisL1: 3D structure…
- PDB
- 7NUD
- Type
- protein
- Length
- 655 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
- LRZ
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 36% 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 | 320 | 28% helix, 36% strand | Q6NZB1 |
Ligands and binding sites
- LRZ · methyl 6-[3-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]propylcarbamoylamino]-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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.75 | 0.83 | 47 | LRZ |
| 2 | 320 | 0.69 | 0.83 | 39 | LRZ |
| 3 | 82 | 0.57 | 0.87 | 17 | empty |
| 4 | 113 | 0.54 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1780 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7NUD · Crystal structure of mouse PRMT6 in complex with inhibitor EML734 · 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 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 7NUD · PDBe 7NUD · UniProt Q6NZB1
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