Research workbench
Structure of TRM8, M7G methylation enzyme
Analyse Structure of TRM8, M7G methylation enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDV
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(7)-)-methyltransferase
- EC
- 2.1.1.33
- UniProt
- Q12009
- Ligands
- SAM
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) | protein | 216 | 38% helix, 22% strand | Q12009 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.70 | 0.81 | 46 | SAM |
| 2 | 407 | 0.69 | 0.81 | 45 | SAM |
| 3 | 175 | 0.48 | 0.76 | 24 | empty |
| 4 | 202 | 0.48 | 0.75 | 29 | empty |
| 5 | 61 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- E–F · 1110 Ų buried · 13 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 Q12009
- Elsewhere: RCSB PDB 2VDV · PDBe 2VDV · UniProt Q12009
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