Research workbench
Human PRMT6 with bound fragment-type inhibitor
Analyse Human PRMT6 with bound fragment-type inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EGS
- Type
- protein
- Length
- 1,344 residues
- Chains
- 4
- 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
- 5NR, SAH
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 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 | 335 | 31% helix, 36% strand | Q96LA8 |
| B | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 338 | 31% helix, 35% strand | Q96LA8 |
| C | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 337 | 32% helix, 35% strand | Q96LA8 |
| D | Protein arginine N-methyltransferase 6 (EC 2.1.1.-, 2.1.1.125) | protein | 334 | 31% helix, 35% strand | Q96LA8 |
Ligands and binding sites
- 5NR · 2-[4-(phenylmethyl)piperidin-1-yl]ethanamine · ligand · 6 copies · chains A, B, C, D
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.74 | 0.86 | 48 | SAH, 5NR |
| 2 | 343 | 0.74 | 0.85 | 50 | SAH, 5NR |
| 3 | 911 | 0.74 | 0.77 | 90 | empty |
| 4 | 373 | 0.72 | 0.84 | 49 | SAH, 5NR |
| 5 | 356 | 0.71 | 0.83 | 46 | SAH, 5NR |
Interfaces
6 interfaces between chains.
- B–C · 1851 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1817 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 582 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 5EGS · PDBe 5EGS · UniProt Q96LA8
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