Research workbench
Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP
Analyse Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DK4
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Geobacillus stearothermophilus
- Molecule
- Tryptophan--tRNA ligase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- ATP, 5BX, MG
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 328 | 56% helix, 8% strand | P00953 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 5BX · (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.79 | 0.86 | 61 | ATP, MG, 5BX |
| 2 | 56 | 0.33 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5DK4 · Crystal structure analysis of tryptophanyl-tRNA synthetase from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P00953 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P00953) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P00953
- Elsewhere: RCSB PDB 5DK4 · PDBe 5DK4 · UniProt P00953
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