Research workbench
Crystal structure of resveratrol bound human tyrosyl tRNA synthetase
Analyse Crystal structure of resveratrol 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
- 4Q93
- Type
- protein
- Length
- 330 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
- STL, SO4, PO4, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase, cytoplasmic (EC 6.1.1.1) | protein | 330 | 55% helix, 12% strand | P54577 |
Ligands and binding sites
- STL · Resveratrol · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.67 | 0.78 | 51 | STL, SO4 |
| 2 | 65 | 0.47 | 0.83 | 15 | empty |
| 3 | 70 | 0.35 | 0.76 | 15 | empty |
| 4 | 72 | 0.34 | 0.75 | 11 | empty |
Compared structures
- 4Q93 · Crystal structure of resveratrol 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 0.96
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 4Q93 · PDBe 4Q93 · UniProt P54577
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