Research workbench
Structure of staphylococcus aureus threonyl-tRNA synthetase complexed with ATP
Analyse Structure of staphylococcus aureus threonyl-tRNA synthetase complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NYR
- Type
- protein
- Length
- 1,279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthetase 1
- EC
- 6.1.1.3
- UniProt
- Q8NW68
- Ligands
- ATP, THR, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase 1 (EC 6.1.1.3) | protein | 642 | 35% helix, 27% strand | Q8NW68 |
| B | Threonyl-tRNA synthetase 1 (EC 6.1.1.3) | protein | 637 | 31% helix, 19% strand | Q8NW68 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- THR · Threonine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.87 | 0.93 | 54 | empty |
| 2 | 418 | 0.74 | 0.84 | 46 | ATP, THR |
| 3 | 381 | 0.72 | 0.83 | 48 | ATP, THR |
| 4 | 641 | 0.71 | 0.78 | 66 | empty |
| 5 | 563 | 0.69 | 0.78 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 2478 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1NYR · Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NW68 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (Q8NW68) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q8NW68
- Elsewhere: RCSB PDB 1NYR · PDBe 1NYR · UniProt Q8NW68
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.