MolNFT v1 · #64781 · protein
Methyltransferase domain of human trimethylguanosine synthase 1 (TGS1) bound to M7GTP and adenosyl-homocysteine (active form)
3GDH · Trimethylguanosine synthase homolog: “Methyltransferase domain of human trimethylguanosine synthase 1 (TGS1) bound to M7GTP and…”. X-ray diffraction, 2 ligands (MGP, SAH), 4 pockets (best druggability 0.75). MolNFT v1 #64781 on…
- PDB
- 3GDH
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimethylguanosine synthase homolog
- EC
- 2.1.1.-
- UniProt
- Q96RS0
- Ligands
- MGP, SAH
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 211 | 44% helix, 21% strand | Q96RS0 |
| B | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 209 | 43% helix, 21% strand | Q96RS0 |
| C | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 207 | 43% helix, 21% strand | Q96RS0 |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- PGR · R-1,2-propanediol · additive · 4 copies · chains A, B, C
- PGO · S-1,2-propanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.75 | 0.86 | 50 | MGP, SAH, PGR |
| 2 | 310 | 0.73 | 0.86 | 47 | MGP, SAH, PGR |
| 3 | 181 | 0.68 | 0.87 | 27 | MGP, PGR |
| 4 | 107 | 0.58 | 0.86 | 28 | SAH |
Interfaces
2 interfaces between chains.
- B–C · 902 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 881 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3GDH · Methyltransferase domain of human Trimethylguanosine Synthase 1 (TGS1) bound to m7GTP and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q96RS0 · AlphaFold monomer V2.0 prediction for trimethylguanosine synthase (Q96RS0) · a predicted model of the same protein · chain C 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 Q96RS0
- Elsewhere: RCSB PDB 3GDH · PDBe 3GDH · UniProt Q96RS0
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