Research workbench
Glutamyl-tRNA synthetase from thermus thermophilus in complex with TRNA(GLU) and L-glutamate
Analyse Glutamyl-tRNA synthetase from thermus thermophilus in complex with TRNA(GLU)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CV0
- Type
- protein + RNA
- Length
- 1,086 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; Glutamyl-tRNA synthetase
- EC
- 6.1.1.17
- UniProt
- P27000
- Ligands
- GLU, MG
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | TRNA | rna | 75 | — | — |
| A, B | Glutamyl-tRNA synthetase (EC 6.1.1.17) | protein | 468 | 53% helix, 12% strand | P27000 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains C, A, D, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.74 | 0.85 | 39 | GLU |
| 2 | 442 | 0.73 | 0.83 | 41 | GLU |
| 3 | 1015 | 0.73 | 0.77 | 46 | empty |
| 4 | 285 | 0.72 | 0.86 | 38 | empty |
| 5 | 1140 | 0.72 | 0.76 | 51 | empty |
Interfaces
2 interfaces between chains.
- D–B · 2356 Ų buried · 54 hydrogen bonds · protein-nucleic
- C–A · 2312 Ų buried · 51 hydrogen bonds · protein-nucleic
Compared structures
- 2CV0 · Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu) and… · the same entry in another collection · chain A against A, TM-score 1.00
- P27000 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase (P27000) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P27000
- Elsewhere: RCSB PDB 2CV0 · PDBe 2CV0 · UniProt P27000
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