MolNFT v1 · #158412 · protein
Type 1 prmt in complex with the inhibitor GSK3368715
6NT2 · Protein arginine N-methyltransferase 1: “Type 1 prmt in complex with the inhibitor GSK3368715”. X-ray diffraction, 2 ligands (SAH, KZS), 6 pockets (best druggability 0.78). MolNFT v1 #158412 on GenesisL1: 3D structure, binding sites…
- PDB
- 6NT2
- Type
- protein
- Length
- 1,320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 1
- EC
- 2.1.1.319
- UniProt
- Q99873
- Ligands
- SAH, KZS
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Protein arginine N-methyltransferase 1 (EC 2.1.1.319) | protein | 330 | 28% helix, 37% strand | Q99873 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, D, B, C
- KZS · N~1~-({5-[4,4-bis(ethoxymethyl)cyclohexyl]-1H-pyrazol-4-yl}methyl)-N~1~,N~2~-dimethylethane-1,2-diamine · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 23 copies · chains A, D, B, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.78 | 0.82 | 67 | SAH, KZS, GOL |
| 2 | 568 | 0.78 | 0.84 | 65 | SAH, KZS, GOL |
| 3 | 505 | 0.77 | 0.84 | 63 | SAH, KZS |
| 4 | 696 | 0.76 | 0.81 | 67 | SAH, KZS, GOL |
| 5 | 421 | 0.56 | 0.73 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–D · 2505 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2438 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NT2 · type 1 PRMT in complex with the inhibitor GSK3368715 · the same entry in another collection · chain B against B, TM-score 1.00
- Q99873 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 1 (Q99873) · a predicted model of the same protein · chain B 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 Q99873
- Elsewhere: RCSB PDB 6NT2 · PDBe 6NT2 · UniProt Q99873
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