MolNFT v1 · #109481 · protein
Crystal structure of protein arginine methyltransferase PRMT8
4X41 · Protein arginine N-methyltransferase 8: “Crystal structure of protein arginine methyltransferase PRMT8”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.60). MolNFT v1 #109481 on GenesisL1: 3D structure, binding…
- PDB
- 4X41
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 8
- EC
- 2.1.1.125
- UniProt
- Q9NR22
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 8 (EC 2.1.1.125) | protein | 311 | 21% helix, 36% strand | Q9NR22 |
| B | Protein arginine N-methyltransferase 8 (EC 2.1.1.125) | protein | 303 | 18% helix, 38% strand | Q9NR22 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.60 | 0.78 | 46 | empty |
| 2 | 263 | 0.59 | 0.79 | 31 | SAH |
| 3 | 122 | 0.47 | 0.79 | 20 | empty |
| 4 | 76 | 0.44 | 0.80 | 19 | empty |
| 5 | 77 | 0.41 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1068 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4X41 · Crystal Structure of Protein Arginine Methyltransferase PRMT8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NR22 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 8 (Q9NR22) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NR22
- Elsewhere: RCSB PDB 4X41 · PDBe 4X41 · UniProt Q9NR22
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.