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Crystal structure of the human PRMT5:MEP50 complex with JNJ44064146

Analyse Crystal structure of the human PRMT5:MEP50 complex with JNJ44064146 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RLL
Type: protein
Length: 928 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: K8H
Pockets: 6 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein arginine N-methyltransferase 5 (EC 2.1.1.320)	protein	625	31% helix, 27% strand	O14744
B	Methylosome protein 50	protein	303	2% helix, 50% strand	Q9BQA1

Ligands and binding sites

K8H · (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-5-(1,8-diazaspiro[4.5]decan-1-ylmethyl)oxolane-3,4-diol · 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	1113	0.88	0.89	116	empty
2	179	0.80	0.95	31	K8H
3	435	0.60	0.75	35	empty
4	147	0.55	0.81	18	empty
5	137	0.50	0.79	23	empty

Interfaces

1 interface between chains.

A–B · 2127 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

6RLL · CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146 · 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 0.98

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 6RLL · PDBe 6RLL · UniProt O14744 · UniProt Q9BQA1

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