MolNFT v1 · #58253 · protein
Complex structure of tRNA methyltransferase TRM1 from aquifex aeolicus with sinefungin
3AXS · Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase…: “Complex structure of tRNA methyltransferase TRM1 from aquifex aeolicus with sinefungin”. X-ray diffraction, 3 ligands (SFG, ZN, SO4), 3 pockets (best druggability 0.61).…
- PDB
- 3AXS
- Type
- protein
- Length
- 387 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase TRM1
- EC
- 2.1.1.32
- UniProt
- O67010
- Ligands
- SFG, ZN, SO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase TRM1 (EC 2.1.1.32) | protein | 387 | 42% helix, 24% strand | O67010 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.61 | 0.85 | 32 | SFG |
| 2 | 88 | 0.36 | 0.75 | 21 | empty |
| 3 | 78 | 0.34 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3AXS · Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with sinefungin · the same entry in another collection · chain A against A, TM-score 1.00
- O67010 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(26)-N(2)/GUANINE(27)-N(2))-dimethyltra… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O67010
- Elsewhere: RCSB PDB 3AXS · PDBe 3AXS · UniProt O67010
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