Research workbench
A novel protein arginine methyltransferase
Analyse A novel protein arginine methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C77
- Type
- protein
- Length
- 402 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase SFM1
- EC
- 2.1.1.-
- UniProt
- Q12314
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase SFM1 (EC 2.1.1.-) | protein | 203 | 32% helix, 21% strand | Q12314 |
| B | Protein arginine N-methyltransferase SFM1 (EC 2.1.1.-) | protein | 199 | 34% helix, 18% strand | Q12314 |
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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.79 | 0.80 | 77 | empty |
| 2 | 273 | 0.63 | 0.81 | 30 | SAH |
| 3 | 276 | 0.60 | 0.79 | 30 | SAH |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- Q12314 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase SFM1 (Q12314) · 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 Q12314
- Elsewhere: RCSB PDB 5C77 · PDBe 5C77 · UniProt Q12314
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