MolNFT v1 · #114803 · protein
M1A58 tRNA methyltransferase mutant - Y78A
5C0O · TRNA (ADENINE(58)-N(1))-methyltransferase trmi: “M1A58 tRNA methyltransferase mutant - Y78A”. X-ray diffraction, 2 ligands (SAM, SO4), 12 pockets (best druggability 0.85). MolNFT v1 #114803 on GenesisL1: 3D structure, binding sites…
- PDB
- 5C0O
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(58)-N(1))-methyltransferase trmi
- EC
- 2.1.1.220
- UniProt
- Q8GBB2
- Ligands
- SAM, SO4
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220) | protein | 238 | 29% helix, 33% strand | Q8GBB2 |
| F | TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220) | protein | 232 | 24% helix, 31% strand | Q8GBB2 |
| G | TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220) | protein | 237 | 31% helix, 29% strand | Q8GBB2 |
| H | TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220) | protein | 211 | 34% helix, 30% strand | Q8GBB2 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains E, F, G, H
- SO4 · Sulfate ion · ion · chains F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.85 | 0.85 | 105 | empty |
| 2 | 111 | 0.79 | 0.98 | 21 | empty |
| 3 | 125 | 0.78 | 0.97 | 26 | empty |
| 4 | 223 | 0.54 | 0.78 | 36 | SAM |
| 5 | 72 | 0.48 | 0.84 | 16 | empty |
Interfaces
6 interfaces between chains.
- E–G · 2336 Ų buried · 48 hydrogen bonds · protein-protein
- F–H · 2293 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 785 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 772 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 188 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
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 Q8GBB2
- Elsewhere: RCSB PDB 5C0O · PDBe 5C0O · UniProt Q8GBB2
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