MolNFT v1 · #17363 · protein
Structure of the predominant protein arginine methyltransferase PRMT1
1OR8 · Protein arginine N-methyltransferase 1: “Structure of the predominant protein arginine methyltransferase PRMT1”. X-ray diffraction, 2 ligands (SAH, UNL), 2 pockets (best druggability 0.59). MolNFT v1 #17363 on GenesisL1: 3D…
- PDB
- 1OR8
- Type
- protein
- Length
- 356 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 1; Substrate peptide
- EC
- 2.1.1.125
- UniProt
- Q63009
- Ligands
- SAH, UNL
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 1 (EC 2.1.1.125) | protein | 313 | 25% helix, 41% strand | Q63009 |
| B | Substrate peptide | protein | 15 | 0% helix, 0% strand | — |
| C | Substrate peptide | protein | 9 | 0% helix, 0% strand | — |
| D | Substrate peptide | protein | 10 | 0% helix, 0% strand | — |
| E | Substrate peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B, C, D
- UNL · Unknown ligand · ligand · 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.59 | 0.80 | 36 | SAH |
| 2 | 88 | 0.52 | 0.84 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 822 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 394 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 44 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1OR8 · Structure of the Predominant protein arginine methyltransferase PRMT1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q63009 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 1 (Q63009) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q63009
- Elsewhere: RCSB PDB 1OR8 · PDBe 1OR8 · UniProt Q63009
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