Research workbench
Crystal structure of glutamyl-tRNA synthetase 1 (ec 6.1.1.17) (glutamate-tRNA ligase 1) (glurs 1) (TM1351) from thermotoga maritima at 2.5 a resolution
Analyse Crystal structure of glutamyl-tRNA synthetase 1 (ec 6.1.1.17) (glutamate-tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O5R
- Type
- protein
- Length
- 468 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-tRNA synthetase 1
- EC
- 6.1.1.17
- UniProt
- Q9X172
- Ligands
- CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) | protein | 468 | 50% helix, 12% strand | Q9X172 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.60 | 0.78 | 35 | CL |
| 2 | 135 | 0.42 | 0.75 | 25 | CL |
| 3 | 94 | 0.36 | 0.74 | 24 | empty |
| 4 | 58 | 0.26 | 0.73 | 20 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2O5R · Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X172 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase 1 (Q9X172) · a predicted model of the same protein · chain A 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 Q9X172
- Elsewhere: RCSB PDB 2O5R · PDBe 2O5R · UniProt Q9X172
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