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Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with TRNA(TYR) and L-tyrosine
Analyse Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with TRNA(TYR)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J1U
- Type
- protein + RNA
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(TYR); Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- Q57834
- Ligands
- TYR, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA(TYR) | rna | 74 | — | — |
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 299 | 52% helix, 13% strand | Q57834 |
Ligands and binding sites
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 | 424 | 0.69 | 0.80 | 44 | TYR |
| 2 | 572 | 0.63 | 0.76 | 29 | MG |
| 3 | 443 | 0.63 | 0.78 | 34 | empty |
| 4 | 115 | 0.40 | 0.76 | 22 | empty |
| 5 | 51 | 0.27 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- B–A · 579 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 1J1U · Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and… · the same entry in another collection · chain B against B, 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 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 1J1U · PDBe 1J1U · UniProt Q57834
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