Research workbench
Crystal structure of glytamyl-tRNA synthetase glurs from pseudomonas aeruginosa
Analyse Crystal structure of glytamyl-tRNA synthetase glurs from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TGT
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate--tRNA ligase
- EC
- 6.1.1.17
- UniProt
- Q9XCL6
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 461 | 52% helix, 11% strand | Q9XCL6 |
| B | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 453 | 53% helix, 12% strand | Q9XCL6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.69 | 0.81 | 45 | GOL |
| 2 | 404 | 0.68 | 0.80 | 47 | SO4 |
| 3 | 318 | 0.55 | 0.75 | 44 | SO4 |
| 4 | 116 | 0.49 | 0.80 | 22 | empty |
| 5 | 97 | 0.47 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5TGT · Crystal structure of glytamyl-tRNA synthetase GluRS from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XCL6 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase (Q9XCL6) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9XCL6
- Elsewhere: RCSB PDB 5TGT · PDBe 5TGT · UniProt Q9XCL6
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