Research workbench
Structure of a novel protein arginine methyltransferase
Analyse Structure of 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
- 5C74
- Type
- protein
- Length
- 355 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
- NI, SO4
- Pockets
- 4 · best druggability 0.70
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 | 211 | 33% helix, 21% strand | Q12314 |
| B | Protein arginine N-methyltransferase SFM1 (EC 2.1.1.-) | protein | 144 | 33% helix, 17% strand | Q12314 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.70 | 0.82 | 43 | empty |
| 2 | 291 | 0.56 | 0.76 | 34 | empty |
| 3 | 100 | 0.43 | 0.78 | 26 | empty |
| 4 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5C74 · Structure of a novel protein arginine methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.95
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 5C74 · PDBe 5C74 · UniProt Q12314
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