Research workbench
Crystal structure of TRM14 from pyrococcus furiosus in complex with sinefungin
Analyse Crystal structure of TRM14 from pyrococcus furiosus in complex with sinefungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TM5
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crystal structure of TRM14
- EC
- 2.1.1.-
- UniProt
- Q8U248
- Ligands
- SFG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crystal structure of TRM14 (EC 2.1.1.-) | protein | 368 | 34% helix, 31% strand | Q8U248 |
| B | Crystal structure of TRM14 (EC 2.1.1.-) | protein | 368 | 32% helix, 30% strand | Q8U248 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.78 | 0.80 | 81 | SFG |
| 2 | 185 | 0.55 | 0.79 | 25 | empty |
| 3 | 189 | 0.52 | 0.78 | 24 | empty |
| 4 | 52 | 0.39 | 0.81 | 13 | empty |
| 5 | 50 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 475 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3TM5 · Crystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin · 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 3TM5 · PDBe 3TM5 · UniProt Q8U248
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