Research workbench
Crystal structure of a M1A58 tRNA methyltransferase
Analyse Crystal structure of a M1A58 tRNA methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PWY
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (adenine-N(1)-)-methyltransferase
- EC
- 2.1.1.36
- UniProt
- Q8GBB2
- Ligands
- SAH, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (adenine-N(1)-)-methyltransferase (EC 2.1.1.36) | protein | 251 | 29% helix, 33% strand | Q8GBB2 |
| B | TRNA (adenine-N(1)-)-methyltransferase (EC 2.1.1.36) | protein | 250 | 30% helix, 34% strand | Q8GBB2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.98 | 24 | empty |
| 2 | 641 | 0.69 | 0.77 | 81 | empty |
| 3 | 169 | 0.49 | 0.77 | 35 | SAH |
| 4 | 160 | 0.47 | 0.77 | 33 | SAH |
| 5 | 57 | 0.40 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2224 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 2PWY · Crystal Structure of a m1A58 tRNA methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GBB2 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase trmi… · a predicted model of the same protein · chain A 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 Q8GBB2
- Elsewhere: RCSB PDB 2PWY · PDBe 2PWY · UniProt Q8GBB2
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