Research workbench
Cryoem structure of PRMT5 bound to covalent pbm-site inhibitor brd- 6988
Analyse Cryoem structure of PRMT5 bound to covalent pbm-site inhibitor brd- 6988 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M05
- Type
- protein
- Length
- 3,636 residues
- Chains
- 8
- Method
- electron microscopy
- 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
- YJG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 615 | 30% helix, 27% strand | O14744 |
| B, D, F, H | Methylosome protein 50 | protein | 294 | 1% helix, 51% strand | Q9BQA1 |
Ligands and binding sites
- YJG · 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-{[2-(pyridin-2-yl)ethyl]sulfamoyl}phenyl)acetamide · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.85 | 0.89 | 61 | empty |
| 2 | 670 | 0.84 | 0.89 | 67 | empty |
| 3 | 861 | 0.84 | 0.87 | 78 | empty |
| 4 | 1024 | 0.84 | 0.85 | 80 | empty |
| 5 | 1016 | 0.82 | 0.84 | 83 | empty |
Interfaces
14 interfaces between chains.
- G–H · 2043 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2025 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2021 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 1651 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7M05 · CryoEM structure of PRMT5 bound to covalent PBM-site inhibitor BRD-6988 · the same entry in another collection · chain H against H, 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 0.97
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 7M05 · PDBe 7M05 · UniProt O14744 · UniProt Q9BQA1
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