Research workbench
Crystal structure of protein arginine methyltransferase PRMT5 in complex with sah
Analyse Crystal structure of protein arginine methyltransferase PRMT5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UA3
- Type
- protein
- Length
- 1,313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5
- EC
- 2.1.1.125
- UniProt
- P46580
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.125) | protein | 662 | 30% helix, 24% strand | P46580 |
| B | Protein arginine N-methyltransferase 5 (EC 2.1.1.125) | protein | 651 | 29% helix, 25% strand | P46580 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.80 | 0.95 | 34 | SAH |
| 2 | 294 | 0.78 | 0.89 | 48 | SAH |
| 3 | 743 | 0.77 | 0.82 | 110 | empty |
| 4 | 53 | 0.65 | 0.94 | 16 | empty |
| 5 | 499 | 0.64 | 0.77 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1766 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3UA3 · Crystal Structure of Protein Arginine Methyltransferase PRMT5 in complex with SAH · the same entry in another collection · chain B against B, TM-score 1.00
- P46580 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 5 (P46580) · a predicted model of the same protein · chain B against A, TM-score 0.56
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 P46580
- Elsewhere: RCSB PDB 3UA3 · PDBe 3UA3 · UniProt P46580
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