MolNFT v1 · #16434 · protein
Structure of staphylococcus aureus threonyl-tRNA synthetase complexed with an analogue of threonyl adenylate
1NYQ · Threonyl-tRNA synthetase 1: “Structure of staphylococcus aureus threonyl-tRNA synthetase complexed with an analogue of threonyl adenylate”. X-ray diffraction, 2 ligands (TSB, ZN), 15 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 1NYQ
- Type
- protein
- Length
- 1,287 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
- TSB, ZN
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonyl-tRNA synthetase 1 (EC 6.1.1.3) | protein | 642 | 34% helix, 23% strand | Q8NW68 |
| B | Threonyl-tRNA synthetase 1 (EC 6.1.1.3) | protein | 645 | 31% helix, 20% strand | Q8NW68 |
Ligands and binding sites
- TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.86 | 0.93 | 54 | empty |
| 2 | 398 | 0.74 | 0.84 | 44 | TSB |
| 3 | 405 | 0.71 | 0.83 | 42 | ZN, TSB |
| 4 | 844 | 0.70 | 0.76 | 70 | empty |
| 5 | 783 | 0.70 | 0.76 | 65 | empty |
Interfaces
1 interface between chains.
- A–B · 2410 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1NYQ · Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with an analogue of… · 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 0.93
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 1NYQ · PDBe 1NYQ · UniProt Q8NW68
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.