Research workbench
Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-10 and ATP
Analyse Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EV3
- Type
- protein
- Length
- 319 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Mycobacterium tuberculosis
- Molecule
- Tryptophan--tRNA ligase
- EC
- 6.1.1.2
- UniProt
- A0A045IZS3
- Ligands
- ATP, JE3, MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 319 | 57% helix, 8% strand | A0A045IZS3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- JE3 · (5S)-5-[(1R)-1-(4-fluoranyl-1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one · ligand · chains A
- MG · Magnesium ion · metal · 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 | 380 | 0.73 | 0.84 | 44 | ATP, MG, JE3 |
| 2 | 55 | 0.27 | 0.73 | 14 | empty |
Compared structures
- 7EV3 · Crystal structure of mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A045IZS3
- Elsewhere: RCSB PDB 7EV3 · PDBe 7EV3 · UniProt A0A045IZS3
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