Research workbench
PRMT5(M420T MUTANT):MEP50 complexed with inhibitor pf-06855800
Analyse PRMT5(M420T MUTANT):MEP50 complexed with inhibitor pf-06855800 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXG
- Type
- protein
- Length
- 1,847 residues
- Chains
- 4
- 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
- ZR4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 625 | 32% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 298 | 2% helix, 52% strand | Q9BQA1 |
| D | Methylosome protein 50 | protein | 299 | 2% helix, 52% strand | Q9BQA1 |
Ligands and binding sites
- ZR4 · 7-[(5R)-5-C-(4-chloro-3-fluorophenyl)-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.83 | 0.84 | 81 | empty |
| 2 | 1054 | 0.83 | 0.84 | 76 | empty |
| 3 | 1119 | 0.81 | 0.83 | 102 | empty |
| 4 | 1166 | 0.80 | 0.82 | 106 | empty |
| 5 | 342 | 0.79 | 0.89 | 47 | ZR4 |
Interfaces
5 interfaces between chains.
- C–D · 2222 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2208 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1631 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 77 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7MXG · PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06855800 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BQA1 · AlphaFold monomer V2.0 prediction for methylosome protein 50 (Q9BQA1) · a predicted model of the same protein · chain D 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 0.97
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 7MXG · PDBe 7MXG · UniProt O14744 · UniProt Q9BQA1
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