MolNFT v1 · #62471 · protein
Methyltransferase domain of human trimethylguanosine synthase TGS1 bound to M7GPPPA (inactive form)
3EGI · Trimethylguanosine synthase homolog: “Methyltransferase domain of human trimethylguanosine synthase TGS1 bound to M7GPPPA (inactive form)”. X-ray diffraction, 1 ligand (ADP), 7 pockets (best druggability 0.71). MolNFT v1 #62471 on…
- PDB
- 3EGI
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimethylguanosine synthase homolog
- EC
- 2.1.1.-
- UniProt
- Q96RS0
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 195 | 32% helix, 28% strand | Q96RS0 |
| B, C | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 192 | 34% helix, 28% strand | Q96RS0 |
| D | Trimethylguanosine synthase homolog (EC 2.1.1.-) | protein | 189 | 34% helix, 29% strand | Q96RS0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.71 | 0.79 | 58 | empty |
| 2 | 678 | 0.68 | 0.76 | 58 | empty |
| 3 | 350 | 0.63 | 0.78 | 43 | empty |
| 4 | 159 | 0.42 | 0.74 | 34 | ADP |
| 5 | 91 | 0.38 | 0.76 | 23 | ADP |
Interfaces
5 interfaces between chains.
- A–B · 835 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 545 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 435 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 281 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3EGI · Methyltransferase domain of human trimethylguanosine synthase TGS1 bound to m7GpppA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96RS0 · AlphaFold monomer V2.0 prediction for trimethylguanosine synthase (Q96RS0) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 3EGI · PDBe 3EGI · UniProt Q96RS0
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