Research workbench
Tyrosyl-tRNA synthetase from thermus thermophilus complexed with tyrosinol
Analyse Tyrosyl-tRNA synthetase from thermus thermophilus complexed with tyrosinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H3F
- Type
- protein
- Length
- 809 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
- P83453
- Ligands
- TYE, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 403 | 47% helix, 16% strand | P83453 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 406 | 48% helix, 16% strand | P83453 |
Ligands and binding sites
- TYE · 4-[(2S)-2-amino-3-hydroxypropyl]phenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.71 | 0.80 | 48 | SO4, TYE |
| 2 | 601 | 0.70 | 0.79 | 57 | SO4, TYE |
| 3 | 152 | 0.60 | 0.84 | 30 | empty |
| 4 | 133 | 0.49 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1304 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1H3F · Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol · the same entry in another collection · chain A against A, TM-score 1.00
- P83453 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (P83453) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P83453
- Elsewhere: RCSB PDB 1H3F · PDBe 1H3F · UniProt P83453
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