MolNFT v1 · #93025 · protein

Crystal structure of the human PRMT5:MEP50 complex

4GQB · Protein arginine N-methyltransferase 5: “Crystal structure of the human PRMT5:MEP50 complex”. X-ray diffraction, 2 ligands (ACE, 0XU), 7 pockets (best druggability 0.85). MolNFT v1 #93025 on GenesisL1: 3D structure, binding sites…

PDB: 4GQB
Type: protein
Length: 936 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein arginine N-methyltransferase 5; Methylosome protein 50; Histone H4 peptide
EC: 2.1.1.-, 2.1.1.125
UniProt: O14744, Q9BQA1, P62805
Ligands: ACE, 0XU
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 3 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	303	2% helix, 51% strand	Q9BQA1
C	Histone H4 peptide	protein	8	0% helix, 25% strand	P62805

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, C
0XU · (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid · ligand · chains A, C

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	760	0.85	0.88	74	empty
2	645	0.83	0.88	67	empty
3	143	0.80	0.97	27	0XU
4	304	0.58	0.77	45	empty
5	193	0.50	0.77	32	empty

Interfaces

2 interfaces between chains.

A–B · 2146 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4GQB · Crystal Structure of the human PRMT5:MEP50 Complex · 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 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
P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain C against A, TM-score 0.42

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
Every structure of UniProt P62805
Elsewhere: RCSB PDB 4GQB · PDBe 4GQB · UniProt O14744 · UniProt Q9BQA1 · UniProt P62805

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