Research workbench
Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM
Analyse Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X61
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- O14744, Q9BQA1
- Ligands
- SAM, 3XV
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.-, 2.1.1.125) | protein | 625 | 32% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 302 | 2% helix, 50% strand | Q9BQA1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- 3XV · N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide · ligand · chains A
- GOL · Glycerol · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.88 | 68 | empty |
| 2 | 642 | 0.83 | 0.87 | 63 | empty |
| 3 | 601 | 0.82 | 0.87 | 58 | SAM, 3XV |
| 4 | 380 | 0.63 | 0.78 | 37 | empty |
| 5 | 155 | 0.52 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2156 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4X61 · Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQA1 · AlphaFold monomer V2.0 prediction for methylosome protein 50 (Q9BQA1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O14744 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 5 (O14744) · 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 O14744
- Every structure of UniProt Q9BQA1
- Elsewhere: RCSB PDB 4X61 · PDBe 4X61 · UniProt O14744 · UniProt Q9BQA1
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