Research workbench
Crystal structure of tyrosyl-tRNA synthetase complexed with P-(2- tetrazolyl)-phenylalanine
Analyse Crystal structure of tyrosyl-tRNA synthetase complexed with P-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N2Y
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- Q57834
- Ligands
- TEF
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 305 | 50% helix, 13% strand | Q57834 |
Ligands and binding sites
- TEF · 4-(2H-tetrazol-2-yl)-L-phenylalanine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.81 | 0.88 | 66 | TEF |
| 2 | 369 | 0.80 | 0.89 | 46 | TEF |
| 3 | 229 | 0.68 | 0.85 | 28 | empty |
| 4 | 194 | 0.65 | 0.85 | 32 | empty |
| 5 | 55 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 780 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3N2Y · Crystal structure of tyrosyl-tRNA synthetase complexed with p-(2-tetrazolyl)-phenylalanine · 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 B against A, TM-score 1.00
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 3N2Y · PDBe 3N2Y · UniProt Q57834
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