MolNFT v1 · #109551 · protein

Crystal structure of PRMT5:MEP50 with EPZ015666 and sinefungin

4X60 · Protein arginine N-methyltransferase 5: “Crystal structure of PRMT5:MEP50 with EPZ015666 and sinefungin”. X-ray diffraction, 2 ligands (SFG, 3XV), 7 pockets (best druggability 0.84). MolNFT v1 #109551 on GenesisL1: 3D structure…

PDB: 4X60
Type: protein
Length: 935 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, 3XV
Pockets: 7 · best druggability 0.84

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	310	2% helix, 50% strand	Q9BQA1

Ligands and binding sites

SFG · Sinefungin · 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 · 3 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	729	0.84	0.88	70	empty
2	530	0.82	0.87	59	SFG, 3XV
3	525	0.81	0.88	47	empty
4	247	0.57	0.78	28	empty
5	371	0.57	0.75	38	empty

Interfaces

1 interface between chains.

A–B · 2149 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

4X60 · Crystal structure of PRMT5:MEP50 with EPZ015666 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 4X60 · PDBe 4X60 · UniProt O14744 · UniProt Q9BQA1

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