Research workbench
Crystal structure of TRM14 from pyrococcus furiosus in complex with S- adenosyl-L-homocysteine
Analyse Crystal structure of TRM14 from pyrococcus furiosus in complex with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TLJ
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine N2-)-methyltransferase TRM14
- EC
- 2.1.1.-
- UniProt
- Q8U248
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA (guanine N2-)-methyltransferase TRM14 (EC 2.1.1.-) | protein | 364 | 34% helix, 29% strand | Q8U248 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.61 | 0.82 | 30 | SAH |
| 2 | 223 | 0.58 | 0.80 | 30 | SAH |
| 3 | 229 | 0.56 | 0.78 | 26 | empty |
| 4 | 189 | 0.55 | 0.79 | 23 | empty |
| 5 | 76 | 0.30 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 145 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3TLJ · Crystal structure of Trm14 from Pyrococcus furiosus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U248 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(6)-N2)-methyltransferase (Q8U248) · a predicted model of the same protein · chain B 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 Q8U248
- Elsewhere: RCSB PDB 3TLJ · PDBe 3TLJ · UniProt Q8U248
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