Research workbench
Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase
Analyse Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DLC
- Type
- protein + RNA
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-RNA (76-mer); Tyrosyl-tRNA synthetase, cytoplasmic
- EC
- 6.1.1.1
- UniProt
- P36421
- Ligands
- YMP, MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | T-RNA (76-mer) | rna | 69 | — | — |
| X | Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) | protein | 339 | 55% helix, 11% strand | P36421 |
Ligands and binding sites
- YMP · O-(adenosine-5'-O-yl)-N-(L-tyrosyl)phosphoramidate · ligand · chains X
- MG · Magnesium ion · metal · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.70 | 0.82 | 46 | MG, YMP |
| 2 | 421 | 0.58 | 0.76 | 29 | empty |
| 3 | 389 | 0.54 | 0.74 | 21 | empty |
| 4 | 96 | 0.40 | 0.76 | 17 | empty |
| 5 | 85 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- Y–X · 485 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 2DLC · Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase · the same entry in another collection · chain X against X, TM-score 1.00
- P36421 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, cytoplasmic (P36421) · a predicted model of the same protein · chain X 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 P36421
- Elsewhere: RCSB PDB 2DLC · PDBe 2DLC · UniProt P36421
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