Research workbench
PRMT5/MEP50 crystal structure with mta and phthalazinone fragment bound
Analyse PRMT5/MEP50 crystal structure with mta and phthalazinone fragment bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S0U
- Type
- protein
- Length
- 910 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
- 81X, MTA, NA, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 614 | 30% helix, 26% strand | O14744 |
| B | Methylosome protein 50 | protein | 296 | 1% helix, 51% strand | Q9BQA1 |
Ligands and binding sites
- 81X · 4-(aminomethyl)phthalazin-1(2H)-one · ligand · chains A
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 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 | 0.82 | 0.84 | 76 | empty |
| 2 | 1072 | 0.81 | 0.83 | 104 | empty |
| 3 | 525 | 0.76 | 0.83 | 66 | 81X, MTA |
| 4 | 93 | 0.52 | 0.83 | 14 | empty |
| 5 | 210 | 0.50 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2226 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 7S0U · PRMT5/MEP50 crystal structure with MTA and phthalazi fragment bound · 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 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 7S0U · PDBe 7S0U · UniProt O14744 · UniProt Q9BQA1
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