Research workbench

PRMT5/MEP50 with compound 29 bound

Analyse PRMT5/MEP50 with compound 29 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SES
Type: protein
Length: 930 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: 2.1.1.320
UniProt: O14744, Q9BQA1
Ligands: 97X, MTA
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein arginine N-methyltransferase 5 (EC 2.1.1.320)	protein	625	32% helix, 26% strand	O14744
B	Methylosome protein 50	protein	305	2% helix, 50% strand	Q9BQA1

Ligands and binding sites

97X · (2P)-2-{4-[4-(aminomethyl)-1-oxo-1,2-dihydrophthalazin-6-yl]-1-methyl-1H-pyrazol-5-yl}naphthalene-1-carbonitrile · ligand · chains A
MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	606	0.84	0.90	66	empty
2	513	0.82	0.89	59	empty
3	352	0.79	0.89	49	97X, MTA
4	595	0.68	0.77	67	empty
5	92	0.38	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 2142 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

7SES · PRMT5/MEP50 with compound 29 bound · the same entry in another collection · chain A against A, TM-score 1.00
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 7SES · PDBe 7SES · UniProt O14744 · UniProt Q9BQA1

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