Research workbench
Crystal structure of 4-(TRIFLUOROMETHYLDIAZIRINYL)PHENYLALANYL-tRNA synthetase
Analyse Crystal structure of 4-(TRIFLUOROMETHYLDIAZIRINYL)PHENYLALANYL-tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D6U
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- Q57834
- Ligands
- T11
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 306 | 51% helix, 13% strand | Q57834 |
Ligands and binding sites
- T11 · 4-[3-(trifluoromethyl)diaziridin-3-yl]-L-phenylalanine · ligand · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.76 | 0.84 | 49 | T11 |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3D6U · Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- Q57834 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q57834) · 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 Q57834
- Elsewhere: RCSB PDB 3D6U · PDBe 3D6U · UniProt Q57834
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