Research workbench
PRMT5 complex bound to covalent pbm inhibitor BRD6711
Analyse PRMT5 complex bound to covalent pbm inhibitor BRD6711 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V0P
- Type
- protein
- Length
- 916 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
- QN4, SFG, CL
- Pockets
- 7 · best druggability 0.88
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 | 621 | 31% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 295 | 2% helix, 52% strand | Q9BQA1 |
Ligands and binding sites
- QN4 · 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-sulfamoylphenyl)acetamide · ligand · chains A
- SFG · Sinefungin · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.88 | 0.89 | 113 | empty |
| 2 | 388 | 0.80 | 0.89 | 52 | SFG |
| 3 | 397 | 0.62 | 0.77 | 52 | empty |
| 4 | 228 | 0.56 | 0.78 | 27 | empty |
| 5 | 145 | 0.49 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2163 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6V0P · PRMT5 complex bound to covalent PBM inhibitor BRD6711 · the same entry in another collection · chain B against B, 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 6V0P · PDBe 6V0P · UniProt O14744 · UniProt Q9BQA1
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