Research workbench
PRMT5/MEP50 crystal structure with mta and an achiral, class 1, non- atropisomeric inhibitor bound
Analyse PRMT5/MEP50 crystal structure with mta and an achiral, class 1, non… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UOH
- Type
- protein
- Length
- 927 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
- NXF, MTA
- Pockets
- 9 · best druggability 0.85
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 2.1.1.320) | protein | 625 | 32% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 302 | 2% helix, 51% strand | Q9BQA1 |
Ligands and binding sites
- NXF · (2M)-2-[(4M)-4-{4-(aminomethyl)-1-oxo-8-[(2R)-oxolan-2-yl]-1,2-dihydrophthalazin-6-yl}-1-methyl-1H-pyrazol-5-yl]-1-benzothiophene-3-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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.85 | 0.88 | 74 | empty |
| 2 | 656 | 0.83 | 0.87 | 64 | empty |
| 3 | 403 | 0.79 | 0.88 | 48 | NXF, MTA |
| 4 | 420 | 0.61 | 0.76 | 48 | empty |
| 5 | 168 | 0.50 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2172 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7UOH · PRMT5/MEP50 crystal structure with MTA and an achiral, class 1, non-atropisomeric… · 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 7UOH · PDBe 7UOH · UniProt O14744 · UniProt Q9BQA1
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