Research workbench
The canonical domain of human asparaginyl-tRNA synthetase
Analyse The canonical domain of human asparaginyl-tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XIX
- Type
- protein
- Length
- 1,692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparagine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.22
- UniProt
- O43776
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparagine--tRNA ligase, cytoplasmic (EC 6.1.1.22) | protein | 422 | 35% helix, 30% strand | O43776 |
| B, C | Asparagine--tRNA ligase, cytoplasmic (EC 6.1.1.22) | protein | 423 | 35% helix, 28% strand | O43776 |
| D | Asparagine--tRNA ligase, cytoplasmic (EC 6.1.1.22) | protein | 424 | 35% helix, 28% strand | O43776 |
Ligands and binding sites
- GOL · Glycerol · additive · 27 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.79 | 0.97 | 32 | empty |
| 2 | 126 | 0.77 | 0.96 | 33 | empty |
| 3 | 803 | 0.72 | 0.78 | 69 | empty |
| 4 | 738 | 0.71 | 0.77 | 66 | GOL |
| 5 | 793 | 0.70 | 0.76 | 77 | GOL |
Interfaces
2 interfaces between chains.
- A–D · 3942 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 3892 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 5XIX · The canonical domain of human asparaginyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- O43776 · AlphaFold monomer V2.0 prediction for asparagine--tRNA ligase, cytoplasmic (O43776) · a predicted model of the same protein · chain D 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 O43776
- Elsewhere: RCSB PDB 5XIX · PDBe 5XIX · UniProt O43776
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