MolNFT v1 · #117456 · protein
Human HMT1 hnrnp methyltransferase-like protein 6 (S. cerevisiae)
5E8R · Protein arginine N-methyltransferase 6: “Human HMT1 hnrnp methyltransferase-like protein 6 (S. cerevisiae)”. X-ray diffraction, 4 ligands (SAH, 5L6, UNX), 5 pockets (best druggability 0.75). MolNFT v1 #117456 on GenesisL1: 3D…
- PDB
- 5E8R
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 6
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q96LA8
- Ligands
- SAH, 5L6, UNX, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 332 | 32% helix, 36% strand | Q96LA8 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 333 | 31% helix, 35% strand | Q96LA8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 5L6 · N-methyl-N-({4-[4-(propan-2-yloxy)phenyl]-1H-pyrrol-3-yl}methyl)ethane-1,2-diamine · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 9 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.75 | 0.86 | 42 | SAH, 5L6 |
| 2 | 273 | 0.74 | 0.87 | 45 | SAH, 5L6, UNX |
| 3 | 63 | 0.43 | 0.82 | 17 | empty |
| 4 | 82 | 0.35 | 0.76 | 20 | empty |
| 5 | 59 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1793 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5E8R · Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) · the same entry in another collection · chain A against A, TM-score 1.00
- Q96LA8 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q96LA8) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q96LA8
- Elsewhere: RCSB PDB 5E8R · PDBe 5E8R · UniProt Q96LA8
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