MolNFT v1 · #76223 · protein
An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity
3QE4 · Tyrosyl-tRNA synthetase: “An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity”. X-ray diffraction, 1 ligand (4CF), 6 pockets (best druggability 0.80). MolNFT v1 #76223 on GenesisL1: 3D structure, binding…
- PDB
- 3QE4
- Type
- protein
- Length
- 613 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
- 4CF
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 307 | 51% helix, 12% strand | Q57834 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 306 | 51% helix, 13% strand | Q57834 |
Ligands and binding sites
- 4CF · 4-cyano-L-phenylalanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.80 | 0.81 | 102 | 4CF |
| 2 | 419 | 0.76 | 0.86 | 52 | 4CF |
| 3 | 448 | 0.63 | 0.77 | 44 | empty |
| 4 | 149 | 0.49 | 0.78 | 22 | empty |
| 5 | 94 | 0.41 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 703 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3QE4 · An evolved aminoacyl-tRNA Synthetase with atypical polysubstrate specificity · 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 0.99
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 3QE4 · PDBe 3QE4 · UniProt Q57834
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