Research workbench
PRMT5(M420T MUTANT):MEP50 complexed with inhibitor pf-06939999
Analyse PRMT5(M420T MUTANT):MEP50 complexed with inhibitor pf-06939999 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXN
- Type
- protein
- Length
- 922 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
- ZR1
- Pockets
- 7 · best druggability 0.83
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 | 621 | 30% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 301 | 2% helix, 50% strand | Q9BQA1 |
Ligands and binding sites
- ZR1 · (1S,2S,3S,5R)-3-{[6-(difluoromethyl)-5-fluoro-1,2,3,4-tetrahydroisoquinolin-8-yl]oxy}-5-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol · ligand · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.83 | 0.84 | 69 | empty |
| 2 | 859 | 0.80 | 0.83 | 82 | empty |
| 3 | 418 | 0.80 | 0.88 | 52 | ZR1 |
| 4 | 373 | 0.61 | 0.77 | 41 | empty |
| 5 | 218 | 0.55 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2273 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7MXN · PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06939999 · 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 7MXN · PDBe 7MXN · UniProt O14744 · UniProt Q9BQA1
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