Research workbench
Crystal structure of tyrosine bound human tyrosyl tRNA synthetase
Analyse Crystal structure of tyrosine bound human 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
- 4QBT
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.1
- UniProt
- P54577
- Ligands
- TYR, K, PO4, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase, cytoplasmic (EC 6.1.1.1) | protein | 329 | 54% helix, 12% strand | P54577 |
Ligands and binding sites
- TYR · Tyrosine · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.69 | 0.81 | 45 | K, TYR, PO4 |
| 2 | 63 | 0.43 | 0.81 | 15 | empty |
| 3 | 50 | 0.27 | 0.73 | 10 | empty |
Compared structures
- 4QBT · Crystal structure of tyrosine bound human tyrosyl tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- P54577 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, cytoplasmic (P54577) · 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 P54577
- Elsewhere: RCSB PDB 4QBT · PDBe 4QBT · UniProt P54577
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.