MolNFT v1 · #117920 · protein
Crystal structure of PRMT5:MEP50 with compound 15 and sinefungin
5EMM · Protein arginine N-methyltransferase 5: “Crystal structure of PRMT5:MEP50 with compound 15 and sinefungin”. X-ray diffraction, 2 ligands (SFG, 5QL), 7 pockets (best druggability 0.85). MolNFT v1 #117920 on GenesisL1: 3D structure…
- PDB
- 5EMM
- Type
- protein
- Length
- 938 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
- SFG, 5QL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 21% 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 | 30% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 313 | 2% helix, 50% strand | Q9BQA1 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- 5QL · ~{N}-[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-3-(oxan-4-ylamino)benzamide · ligand · chains A
- GOL · Glycerol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.85 | 0.88 | 75 | empty |
| 2 | 638 | 0.82 | 0.87 | 67 | empty |
| 3 | 493 | 0.81 | 0.87 | 53 | SFG, 5QL |
| 4 | 427 | 0.65 | 0.78 | 46 | GOL |
| 5 | 155 | 0.50 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2170 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5EMM · Crystal structure of PRMT5:MEP50 with Compound 15 and sinefungin · 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 0.98
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 O14744
- Every structure of UniProt Q9BQA1
- Elsewhere: RCSB PDB 5EMM · PDBe 5EMM · UniProt O14744 · UniProt Q9BQA1
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