Research workbench
Crystal structure of arginyl-tRNA synthetase complexed with L- canavanine
Analyse Crystal structure of arginyl-tRNA synthetase complexed with L- canavanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q2X
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.19
- UniProt
- P54136
- Ligands
- GGB
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19) | protein | 582 | 53% helix, 12% strand | P54136 |
| B | Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19) | protein | 582 | 52% helix, 11% strand | P54136 |
Ligands and binding sites
- GGB · L-canavanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.74 | 0.81 | 39 | empty |
| 2 | 72 | 0.66 | 0.93 | 19 | empty |
| 3 | 345 | 0.63 | 0.79 | 38 | empty |
| 4 | 244 | 0.63 | 0.81 | 49 | GGB |
| 5 | 67 | 0.61 | 0.91 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4Q2X · Crystal structure of Arginyl-tRNA synthetase complexed with L-canavanine · the same entry in another collection · chain B against B, TM-score 1.00
- P54136 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase, cytoplasmic (P54136) · 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 P54136
- Elsewhere: RCSB PDB 4Q2X · PDBe 4Q2X · UniProt P54136
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