Research workbench
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction
Analyse The active site of yeast aspartyl-tRNA synthetase: structural and functional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ASZ
- Type
- protein + RNA
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-RNA (75-mer); Aspartyl-tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- P04802
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, S | T-RNA (75-mer) (EC 6.1.1.12) | rna | 75 | — | — |
| A, B | Aspartyl-tRNA synthetase | protein | 490 | 30% helix, 24% strand | P04802 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains R, A, S, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.82 | 0.89 | 62 | ATP |
| 2 | 525 | 0.80 | 0.87 | 58 | ATP |
| 3 | 1038 | 0.80 | 0.82 | 71 | empty |
| 4 | 742 | 0.79 | 0.84 | 50 | empty |
| 5 | 1053 | 0.78 | 0.80 | 77 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4688 Ų buried · 90 hydrogen bonds · protein-protein
- S–B · 2173 Ų buried · 68 hydrogen bonds · protein-nucleic
- R–A · 2141 Ų buried · 53 hydrogen bonds · protein-nucleic
- S–A · 30 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 16 modified (nucleotide modification).
Compared structures
- 1ASZ · The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of… · the same entry in another collection · chain R against R, TM-score 1.00
- P04802 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase, cytoplasmic (P04802) · 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 P04802
- Elsewhere: RCSB PDB 1ASZ · PDBe 1ASZ · UniProt P04802
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